The Al-Aqsa Mosque (Arabic: Al-Masjid Al-Aqsa, commonly refers to the southern part of the complex of religious buildings in Jerusalem known as either Al-Haram al-Qudsi al-Sharif (the Noble Sanctuary) to Arabs and Muslims, although in reality the whole area of the Noble Sanctuary is considered Al-Aqsa Mosque and the entire precincts inviolable according to Islamic law. It is known as Har ha-Bayit (the Temple Mount) to Jews and some Christians. It is located in East Jerusalem, a disputed territory governed as part of Israel since its annexation in 1967 but claimed by the Palestinian Authority as part of a future State of Palestine. The largest mosque in Jerusalem, its congregation building can accommodate about 5,000 people worshipping inside it, while the whole Al-Aqsa Mosque compound area may accomodate hundreds of thousands. The government of Israel has granted a Muslim Council, Waqf, full administration of the site. Since the beginning of Al-Aqsa Intifada in 2000, non-Muslims are barred from entering the site.
The congregation building of Al-Aqsa Mosque is sometimes referred to as Jami al-Masjid al-Aqsa or al-Masjid al-Qibli. The term al-Masjid Al-Aqsa proper is the general and oldest name for the precinct of al-Haram al-Qudsi al-Sharif. The name al-Haram al-Qudsi al-Sharif was coined later by the Mamluks.
Origin of name
The name "Al-Aqsa Mosque" translates to "the farthest mosque" ("the remote mosque" according to some translations, such as that of Muhammad Asad), and is associated with the Isra and Mi'raj, a journey made around 621 by the Islamic Prophet Muhammad (c. 570-632) on the winged steed Buraq, which was brought to him by the Archangel Gabriel. This is often referred to in English as Muhammad's "night journey". According to Qur'anic verse, Muhammad took the journey in a single night from "the sacred mosque" (in Mecca) to "the farthest mosque" (al-Masjid al-Aqsa). From a rock there, Muhammad ascended to heaven, accompanied by Gabriel, touring heaven and receiving the commandments, including the five daily prayers, before returning to Earth and back to Mecca to communicate them to the faithful.
The hadith narrator Imam Muslim reports that the Prophet's companion Anas ibn Malik mentions that the Prophet said:
I came to the Buraq, I rode it until we arrived at Bayt al-Maqdis. I tied it to where the Prophets tie, then I entered the masjid I prayed two Rakaah, and then ascended to the heavens.
This story was to become the raison d'etre for Islam's two most important shrines in Jerusalem, the Al Aqsa Mosque and Dome of the Rock, and the driving force behind Muslim ambitions to rule the city to this day.
In this regard, the leading muslim scholar Ibn Taymiyah reports:
al-Masjid al-Aqsa is a name that refers to the whole area of the masjid that was built by Suleiman Peace Be Upon him. Some people today use the term to refer to the prayer house built by Umar bin al-Khattab at the front of this area... When Umar asked Kaab: Where to buid a prayer house for the muslims. Kaab replied: behind the Rock. Umar said: No, but I will build it in front of the Rock because we always pray at the front of mosques. Therefore, Imams usually if they enter the masjid area, they gather people and stand to lead the prayers in the house built by Umar.
The muslims scholar al Tabari reports in Tarikh al-Tabari:
Umar Ibn al-Khattab asked Kaab: Where should we pray? He said: towards the Rock. Umar replied: Oh, Kaab! You are glorifying Judaism. But I will make the Qibla of this masjid at its front just like the Prophet of Allah made the Qibla of all our masajid at its front.
Regarding the name, other sources mention the following:
"Originally the term al-Masjid al-Aqsa was used to refer to the whole area of al-Haram al-Qudsi al-Sharif with all what it holds from establishments including the Dome of the Rock built by Abd al-Malik ibn Marwan in 72 Hijri/691 A.D., which is considered among the most notable Islamic structures. Today, the term al-Masjid al-Aqsa is also used to refer to the large Mosque in the southern part of al-Haram al-Qudsi." ... "The Dome of the Rock structure resides at the heart of al-Masjid al-Aqsa, in the southeaster part of the Old City of Jerusalem, which is wide rectangular area extending 480 meters from the north to the south, and from the east to the west about 300 meters. This area constituites what is almost fifth of the Old City."
According to the teachings of Islam, God in the the Qur'an used the word Mosque when referring to the sites established by Abraham and his children as houses of worship to God centuries before the revelation of the Qur'an. The first of these spots is al-Masjid al-Haram in Mecca and the second is al-Masjid al-Aqsa in Jerusalem. Before Mecca and Jerusalem came under muslim control in 630 A.D. and 638 A.D., the site of al-Masjid al-Haram had the Kaabah which was established by Abraham and Ishmael but at the time of Muhammad was used by pagans. In Jerusalem the site of al-Masjid al-Aqsa, which was under Roman control, was an abandoned and abused area by the Romans but on which a house of worship established originally by the prophet Jacob forty years after his grandfather Abraham established the Kaabah and was used by succeeding prophets like David, Solomon, and Zacharia.
The story of Abraham and Ishmael is mentioned in Qur'an as follows:
22:26 For, when We assigned unto Abraham the site of this House, [We said unto him:] "Do not ascribe divinity to aught beside Me!" and: "Purify My House for those who will walk around it, and those who will stand before it [in meditation], and those who will bow down and prostrate themselves [in prayer]."
Waith bawwana liibraheema makana albayti an la tushrik bee shayan watahhir baytiya lilttaifeena waalqaimeena waalrrukkaAAi alssujoodi
2:127 And remember Abraham and Isma'il raised the foundations of the House (With this prayer): "Our Lord! Accept (this service) from us: For Thou art the All-Hearing, the All-knowing.
Waith yarfaAAu ibraheemu alqawaAAida mina albayti waismaAAeelu rabbana taqabbal minna innaka anta alssameeAAu alAAaleemu
Abu Dharr [ra] is quoted as saying, I asked the beloved Prophet Muhammad [peace be upon him] which was the first mosque on earth? "The Sacred Mosque (in Makkah)," he said. And then which, I asked? 'Masjid al Aqsa,' he said. I further asked, what was the time span between the two? 'Forty years,' the Prophet [peace be upon him] replied. (Imam Muslim)
Al-Aqsa mosque or the Holy Temple is mentioned explicitly in one verse of the Koran and alluded several others. Some of the verses are shown here in the order in which they appear in the Quran rather than the order in which they were revealed to the Prophet Muhammad:
3:37 And thereupon her Sustainer accepted the girl-child with goodly acceptance, and caused her to grow up in goodly growth, and placed her in the care of Zachariah. Whenever Zachariah visited her in the sanctuary [of the Mosque], he found her provided with food. He would ask: "O Mary, whence came this unto thee?" She would answer: "It is from God; behold, God grants sustenance unto whom He wills, beyond all reckoning."
Fataqabbalaha rabbuha biqaboolin hasanin waanbataha nabatan hasanan wakaffalaha zakariyya kullama dakhala AAalayha zakariyya almihraba wajada AAindaha rizqan qala ya maryamu anna laki hatha qalat huwa min AAindi Allahi inna Allaha yarzuqu man yashao bighayri hisabin
3:39 Thereupon, as he stood praying in the sanctuary [of the Mosque], the angels called out unto him: "God sends thee the glad tiding of [the birth of] John, who shall confirm the truth of a word from God, and [shall be] outstanding among men, and utterly chaste, and a prophet from among the righteous."
Fanadathu almalaikatu wahuwa qaimun yusallee fee almihrabi anna Allaha yubashshiruka biyahya musaddiqan bikalimatin mina Allahi wasayyidan wahasooran wanabiyyan mina alssaliheena
17:1 LIMITLESS in His glory is He who transported His servant by night from the Inviolable House of Worship [at Mecca] to the Remote House of Worship [,at Jerusalem] - the environs of which We had blessed -so that We might show him some of Our symbols: for, verily, He alone is all-hearing, all-seeing.
Subhana allathee asra biAAabdihi laylan mina almasjidi alharami ila almasjidi alaqsa allathee barakna hawlahu linuriyahu min ayatina innahu huwa alssameeAAu albaseeru
17:7 [And We said:] "If you persevere in doing good, you will but be doing good to yourselves; and if you do evil, it will be [done] to yourselves." And so, when the prediction of the second [period of your iniquity] came true, [We raised new enemies against you, and allowed them] to disgrace you utterly, and to enter the Mosque [Temple] as [their forerunners] had entered it once before, and to destroy with utter destruction all that they had conquered.
In ahsantum ahsantum lianfusikum wain asatum falaha faitha jaa waAAdu alakhirati liyasoooo wujoohakum waliyadkhuloo almasjida kama dakhaloohu awwala marratin waliyutabbiroo ma AAalaw tatbeeran
19:11 Thereupon he came out of the sanctuary unto his people and signified to them [by gestures]: "Extol His limitless glory by day and by night!"
Fakharaja AAala qawmihi mina almihrabi faawha ilayhim an sabbihoo bukratan waAAashiyyan
38:21 AND YET, has the story of the litigants come within thy ken - [the story of the two] who surmounted the walls of the sanctuary [in which David prayed]?
Wahal ataka nabao alkhasmi ith tasawwaroo almihraba
Restoration of the Mosque site by Omar
Before Jerusalem came under the control of muslims in 638 A.D., it was widely understood that al-Aqsa mosque is the same as David's sanctuary. When Omar bin al-Khattab was given the key to the city by the Patriarch of Jerusalem, Sophronius, he signed with him a treaty that is known as the "Covenant of Omar" and he later asked the Patriarch of Jerusalem to show him what Omar spelled out as 'Masjid Dawood' (Mosque of David). This was called David's sanctuary or prayer niche (mihrab Dawud), in the Qur'an (38:21). David chose the site on which Solomon built his temple. It was an abandoned place and abused by the Romans and the Church at the time. The Patriarch took him to the door of the sanctuary which was almost blocked due to the trash that was placed at the door. Omar looked left and right and said: "Allah is Great, I swear by the one who hold my soul in his hand that this is the Mosque of David which the prophet of Allah described to us after his night journey.' The Caliph Omar started cleaning up the place. He asked Kaab al-Ahbar, who was a Jewish Rabbi that has converted to Islam and came with Omar from Medina, to guide him to the place of the Rock. Omar used his cloths to remove the trash covering the Rock, and other muslims did what Omar was doing. After cleaning up the place, Omar went to the al-Mihrab (a chamber inside the Mosque where the Imam usually stands) and started praying and reading Surat Sad from Quran.
Construction of the Congregational Mosque
The term the farthest mosque is considered in Islamic tradition as the general name for the precinct of al-Haram al-Sharif ("The Noble Sacred Enclosure") in Jerusalem, as well as the specific name for the congregational mosque located at its southern edge.
Umar (c. 581-644), the Muslim caliph who conquered Jerusalem in 637, wanted a place of prayer that does not infringe on nearby Christian and Jewish worship places. That place, to the south of the rock, was developed into a mosque. Sometime between 687-691, Caliph Abd al-Malik built a shrine over the sacred rock, and it was named Qubbat As-Sakhrah, which means "The Dome of the Rock." Some years later, in 709-715, Umayyad caliph al-Walid, son of Abd al-Malik, built, renovated, and expanded the mosque south of the Dome, and at this time called the mosque al-masjid al-aqsa, which means "the farthest mosque".
The contemporary congregational mosque of al-Aqsa is a result of different stages of construction and renovations. It is usually agreed upon that 'Abd al-Malik (685-705), the [[Umayyad Caliph who was the patron of the Dome of the Rock, started the construction of al-Aqsa Mosque at the end of the 7th century. A major building phase took place during the time of the caliphate of his son, al-Walid (709-715). The building suffered from several major earthquakes and was renovated and reconstructed during the Abbasid period by Caliph al-Mahdi (775-785) and possibly by Caliph al-Mansur (754-775).
A further reconstruction was executed during the Fatimid period, in the 11th century. During the Crusader Kingdom of Jerusalem the mosque was considered as Templum Salomonis (Royal Palace of Solomon) and it served as the palace of the Kings of Jerusalem and later as the dwelling place of the Knights Templars. At the same time the Dome of the Rock was regarded as the Templum Domini (The Temple of the Lord). Moreover, several major restorations are known to have taken place during the 14th and 20th century.
The building became known as Masjid al-Aqsa, (Al-Aqsa Mosque), although in reality the whole area of the Noble Sanctuary is considered Al-Aqsa Mosque, the entire precincts inviolable according to Islamic law. Every Friday prayer, the Al-Aqsa Mosque building overflows, with thousands of worshippers who must make their prayers outside in the courtyards of the vast open expanse of the Noble Sanctuary.
Damage from earthquakes in 1927 and 1936 necessitated an almost complete rebuilding of the mosque, in the process of which ancient sections of the original mosque were brought to light.
It has been modified several times to protect it from earthquakes, which sometimes occur in the area, and to adapt to the changing needs of the local population. The form of the present structure has remained essentially the same since it was reconstructed by the Khalif Al-Dhahir in 1033 AD. It is said that he did not alter it from the previous architecture except to narrow it on each side.
Analysis of wooden beams and panels removed from the building during renovations in the 1930s shows they are made from Cedar of Lebanon and Cyprus. Radiocarbon dating indicates a large range of ages, some as old as 9th century BC, showing that some of the wood had previously been used in older buildings.
Mark Twain during his travels in Jerusalem wrote that parts of the Al Aqsa Mosque used stones excavated from the Mount and which were a part of the Jewish Temple :
"Every where about the Mosque of Omar are portions of pillars, curiously wrought altars, and fragments of elegantly carved marble--precious remains of Solomon's Temple. These have been dug from all depths in the soil and rubbish of Mount Moriah, and the Moslems have always shown a disposition to preserve them with the utmost care.... to enter the Mosque of Omar and see the costly marbles that once adorned the inner Temple was annulled. The designs wrought upon these fragments are all quaint and peculiar, and so the charm of novelty is added to the deep interest they naturally inspire. One meets with these venerable scraps at every turn, especially in the neighboring Mosque el Aksa, into whose inner walls a very large number of them are carefully built for preservation. These pieces of stone, stained and dusty with age, dimly hint at a grandeur we have all been taught to regard as the princeliest ever seen on earth; and they call up pictures of a pageant that is familiar to all imaginations--camels laden with spices and treasure--beautiful slaves, presents for Solomon's harem--a long cavalcade of richly caparisoned beasts and warriors--and Sheba's Queen in the van of this vision of "Oriental magnificence.".
Since part of the mosque's extended surrounding wall is the Western Wall venerated by Jews, this relatively small spot in Jerusalem is a source of friction. There have been times when Muslims worshipping at the mosque threw rocks downward at the Jews below at the Western Wall. A group of Jews known as the Temple Mount Faithful have expressed a desire to rebuild the ancient Jewish Temple in that area.
In the morning of August 21, 1969, a fire at Masjid al-Aqsa, gutted the southeastern wing of the mosque. The fire destroyed a priceless one-thousand-year-old wood and ivory pulpit (minbar) that had been sent from Aleppo by Saladin. The "twin" of this minbar (Saladin had them both made at the same time) is still extant in the mosque at the Cave of the Patriarchs in Hebron.
Michael Dennis Rohan, a tourist from Australia, was arrested for the arson attack on August 23, 1969. Rohan was a Protestant follower of an evangelical sect known as the Church of God. By his own admission, Rohan hoped to hasten the coming of the Messiah by burning down the al-Aqsa Mosque. Rohan told the court that he acted as "the Lord's emissary" on divine instructions, in accordance with the Book of Zechariah, and that he had tried to destroy the al-Aqsa Mosque in order to rebuild the Jewish Temple on the Temple Mount. He was hospitalized in a mental institution, found to be insane and was later deported from Israel.
The Al-Aqsa Intifada is named after the mosque (due to Ariel Sharon's controversial visit to the Temple Mount in September 2000), as are the Al-Aqsa Martyrs' Brigades.
Israeli authorities have foiled the terrorist organization Makhteret's plans to blow up the al-Aqsa Mosque, Makhteret is a branch of the right-wing Jewish organization Kach.
Some Muslims have accused Israel of weakening the walls of the mosque during archaeological excavations that began in 1967 and continue today. In response to concerns about the structure's stability, renovations are being carried out by the Islamic Waqf Foundation. Jews and Israel claim that the Waqf are performing irresponsible excavations weakening the structures stability and destroying Temple Relics and other historical artifacts.  (Hebrew)
The Muslim Waqf is in charge of the Al Aqsa mosque, along with most of the important Muslim shrines in Israel.
The mosque consists today of a seven bay hypostyle hall with several additional small halls to the west and east of the southern section of the building. Unlike most hypostyle-style mosques the building does not have a clearly delineated courtyard unless one considers the whole Haram as its court. It is capped with a silver dome, made of lead sheets, which together with the golden dome of the Dome of the Rock, formulate the icon of the Haram in Jerusalem.
The historical significance of Al-Aqsa Mosque is further emphasised by the fact that Muslims used to turn towards Al-Haram al-Sharif when they prayed.
As it was the place at which Muhammad performed the first commanded prayer after Isra and Mi'raj, it became the qibla (direction) that Muslims faced during prayer and continued to be so for sixteen or seventeen months, 6:60:13. After a revelation recorded in the Koran the qibla was then turned towards Mecca:
We have seen you turning your face about the sky (searching for the right direction). We now assign a qibla that is pleasing to you. Henceforth, you shall turn your face towards the Sacred Mosque. Wherever you may be, all of you shall turn your faces towards it. Those who received the previous scripture, know that this is the truth from their Lord. God is never unaware of anything they do. Even if you show the followers of the scripture every kind of miracle, they will not follow your qibla. Nor shall you follow their qibla. They do not even follow each others qibla. If you acquiesce to their wishes, after the knowledge that has come to you, you will belong with the transgressors. (Koran 2:144;145)
For this reason Al-Haram al-Sharif, including the Al-Aqsa Mosque, is known to Muslims as the "First of the Two Qiblas".
The altering of the qibla was precisely the reason Caliph Umar, despite identifying the Rock upon his arrival at the Temple Mount in 638 neither prayed facing it nor built any structure upon it. This was because the significance of that particular spot on the Temple Mount was over in Islamic jurisprudence after the change of qibla event in Islamic ideology. However, because of the holiness of Temple Mount itself Caliph Umar did make a small mosque in the southern corner of its platform which initially was called 'mosque of Umer' and today is known as "Masjid Al-Aqsa", taking caution to avoid the Rock to come between the mosque and the direction of Kaaba so that Muslims would face only Mecca when they prayed 
In another illustration of how significance of the 'first qibla' was diminished in Islam, the following hadith states:
Narrated 'Abdullah bin 'Umar: People say, "Whenever you sit for answering the call of nature, you should not face the qibla or Bait-ul-Maqdis (Jerusalem)." I told them. "Once I went up the roof of our house and I saw Allah's Apostle answering the call of nature while sitting on two bricks facing Bait-ul-Maqdis (See Holy Temple, Hebrew: ??? ?????, Bet HaMikdash)...1:4:147
The importance of Al-Aqsa in Islam
Masjid-al-Aqsa is one of the holiest site in Islam because it belongs to the history of Islam since Abraham until now. It is where, according to Muslims, Abraham (the patriarch of the Abrahamic faiths) established his covenant with God and spread the teaching of monotheism. Muslims respect all the Prophets revered by Judaism and Christianity and their venerated places are also central to the ethos of Islam. Solomon was a prophet and revered by Muslims.
Judaism belief in the Temple of Solomon (Haykal Sulaiman) as the Noble Sanctuary is coherent with the Islam believe in Masjid al-Aqsa because the literal meaning of masjid does not mean a building or any specific place. The word Masjid derived from the root word "Saa" "Jaa" "Daa" in arabic which means (to prostrate) (act of worship). In this case not only the Mosque of Umar is considered as Masjid al-Aqsa but the entire precinct too. Muslims belief that the Temple of Solomon meant by the Jews was a Masjid and not a temple because Islam believe that all prophet conveyed the same messege and prostrated to God during prayers.
It was the site where Muhammad ascended to heaven during Isra and Mi'raj. (The main place, however, where Muhammad received most revelations, including the first, was in the cave of Hira where he meditated frequently during the first forty years of his life.)
The Mosque of Umar reminds all about the atrocity and devestation suffered by the inhabitant of Jerusalem during the Roman occupation. It also signifies freedom of religion achieved by Jews, Christians and Muslims a long time before.
It was the first qibla, the second house of God after Kaabah in Mecca, and the third holiest site in Islam.
Second house of prayer established on Earth
Imam Muslim quotes Abu Dharr as saying:
"I asked the beloved Prophet Muhammad which was the first "mosque" [i.e. house of prayer] on Earth?"
"The Sacred House of Prayer (Masjid al-Haram), i.e. Kaaba)", he said.
"And then which", I asked?
"The Furthest House of Prayer (Masjid al Aqsa, i.e. Holy Temple)", he said.
I further asked, "what was the time span between the two?"
"Forty years", the Prophet replied.
Third sacred mosque by its virtue
The Sahih Bukhari quotes Abu al-Dardaa as saying: "the Prophet of Allah Muhammad said a prayer in the Sacred Mosque (in Mecca) is worth 100,000 prayers; a prayer in my mosque (in Medina) is worth 1,000 prayers; and a prayer in al-Masjid al-Aqsa is worth 500 prayers more than in an any other mosque.
Abu Huraira [ra] is quoted as saying that Allah's Messenger [peace be upon him] said, "set out deliberately on a journey only to three mosques: this mosque of mine (in Medina), the Sacred Mosque (in Makkah) and the Masjid al Aqsa (in Jerusalem) (Bukhari & Muslim)
As part of another tradition, on the authority of Maimunah bint Sa'd, it is reported that, upon being asked about a person who is unable to travel to the Al-Aqsa Mosque he replied: "The Messenger of Allah (Muhammed) said, "He should make a gift of oil to be burnt therein, for he who gives a gift to the Al-Aqsa Mosque will be like one who has prayed Salaah (five daily ritual prayers of Islam) therein." 
Location of the "farthest mosque"
The "farthest mosque" in verse 17:1 of the Qur'an is traditionally interpreted by Muslims as referring to the site at the Noble Sanctuary in Jerusalem on which the mosque of that name now stands. According to this tradition, the term used for mosque, "masjid", literally means "place of prostration", and includes monotheistic places of worship such as Solomon's Temple, which in verse 17:7 (in the same sura) is described as a "masjid". Many Western historians regard this as the originally intended interpretation, for instance Heribert Busse  and Neal Robinson 
However some disagree arguing that at the time this verse of the Qur'an was recited (traditionally at around the year 621), many Muslims understood the phrase "furthest mosque" as a poetic phrase for either a mosque established as an exclusively Muslim place of worship - in existence during Muhammad's lifetime - (such as Medina , Jirana , or Kufa ), or a mosque in Heaven, or as a metaphor.
A number of factors are enumerated why they find it unlikely that this verse referred to a location in Jerusalem. 
There were already two places that Muslim tradition of that time period called "the farthest mosque"; one was the mosque in Medina  and the other was the mosque in the town of Jirana, which Muhammed is said to have visited in 630 
Even over a century later, Islamic scholars continued to locate the "farthest mosque" with a site inside Arabia, such as al-Waqidi who in his 9th-century book Kitab al-Tarikh wa al-Maghazi (Book of History and Campaigns) preserved the tradition locating it in Jirana
No mosque existed in Jerusalem during Muhammad's lifetime. It was 6 years after Muhammad's death that the Muslims conquered Jerusalem. Only then were the foundations of the mosque laid by the Second Khalif Umar ibn al-Khattab while he was in Jerusalem. The actual Mosque was completed by Abd al-Malik ibn Marwan and his son Al-Walid I, 68 years after Muhammad's death.
A passage from the biography of Umar ibn al-Khattab states:
The Patriarch of Jerusalem handed over the keys of the city of Jerusalem to Umar. The Muslims were now the masters of Jerusalem. As Umar entered the city he was greeted by the citizens with great enthusiasm. Umar said that he wanted to be led to some place where he could offer thanksgiving prayer to God. He was led to a church but refused to pray there on the ground that that would set a precedent for the Muslims of the following generations to forcibly convert churches into mosques... Umar stayed in Jerusalem for a few days.he founded a mosque at an elevated place in the city. This mosque came to be known as Umar's Mosque.
The above passage informs us that there was no mosque in Jerusalem to pray in when Umar entered the city. He laid the foundation of the first ever mosque in Jerusalem.
The Koranic inscriptions that make up a 240-meter mosaic frieze inside the Dome of the Rock do not include Sura 17:1 and the story of the Night Journey, suggesting that as late as 692 the idea of Jerusalem as the lift-off for the Night Journey had not yet been established. This is a strange omission since Muslims claim that the Dome of the Rock was erected in commemoration of this alleged event. The inscriptions that do mention the Night Journey are later additions made by Abdul Hamid II in 1876, nearly eleven centuries later.
Muhammad ibn al-Hanafiya (638-700), a close relative of Muhammad, is quoted denigrating the notion that the prophet ever set foot on the Rock in Jerusalem: "these damned Syrians," by which he means the Umayyads, "pretend that God put His foot on the Rock in Jerusalem, though [only] one person ever put his foot on the Rock, namely Abraham."
Thus he asserts Muhammad never acended to heaven from the Rock in Jerusalem and that another location was indeed meant by the "farthest mosque".
When Muslims finally did conquer and occupy Jerusalem, they are not known to have identified the Temple Mount with "the farthest mosque" until 715. According to A.L. Tibawi, a Palestinian historian, in 715 the Umayyads built a new mosque on the Temple Mount; they named this Mosque al-masjid al-aqsa, or "farthest mosque" in order to "give reality to the figurative name used in the Koran."
In October 2003 an Egyptian government-owned weekly questioned the sanctity of Jerusalem to Muslims, pointing out that the Prophet Muhammad never made the miraculous "night journey " to the city. According to Al-Qahira, which is published by the Egyptian Ministry of Culture, the two mosques on the Temple Mount were built only to divert the pilgrimage from Mecca in the context of political rivalry between Muslim leaders:
When Abed al-Malik ibn Marwan became caliph and his rival Ibn al-Zubayr held control of Hejaz, he feared that the people would be inclined towards him [Ibn al-Zubayr] when they made pilgrimage [to Mecca], because the only way they could enter Mecca and Medina was with Ibn al- Zubayr's permission and under his control... Therefore, Abd al-Malik prevented people from making pilgrimage until [Ibn al-Zubayr was defeated and] the war ended. He began to build a large mosque in Jerusalem... It is from this point in time that some transmitters of traditions started to promote the religious significance of this mosque and turn it into the 'third to the two holy mosques' [of Mecca and Medina].
The article written by Egyptian columnist Ahmed Arafeh rejects the established Islamic doctrine that Muhammad's celebrated night journey took him from Mecca to Jerusalem. He argues that the journey mentioned in the Koran's Surat al-Isra does not refer to a miraculous journey from Mecca to Jerusalem, but to the prophet's emigration from Mecca to Medina.
There is an opinion among some Muslim scholars that "the farthest mosque" in Qur'an actually points to the Temple of Solomon and not Masjid Al-Aqsa, which was built by Omer Bin Khattab (c. 581-644), the Muslim caliph who conquered Jerusalem in 637. However this had been destroyed many centuries earlier. 
Even if Jerusalem was indeed intended, it was nevertheless a miraculous occurrence, raising doubts whether Muhammed had ever physically set foot in Jerusalem at all. This could be supported by the hadith which states:
The Prophet said, "When the Quraish disbelieved me (concerning my night journey), I stood up in Al-Hijr (the unroofed portion of the Ka'ba) and Allah displayed Bait-ul-Maqdis (Jerusalem) before me, and I started to inform them (Quraish) about its signs while looking at it." 6:60:233
Not only was it proving problematic for Muhammad himself to convince the masses of his journey, but had he indeed visited Jerusalem he should have been able to rely on his memory to describe Jerusalem, not on Allah "displaying it before him".
It is widely believed amongst Muslims that the Night Journey was a physical journey of Muhammad, but some Islamic scholars consider it as a dream. They point to a verse in Qur'an: ...and We did not make the vision which We showed you but a trial for men... 17:60 and a hadith regarding the Night Journey in Sahih Bukhari: ...Allah's Apostle said, "O Moses! By Allah, I feel shy of returning too many times to my Lord." On that Gabriel said, "Descend in Allah's Name." The Prophet then woke while he was in the Sacred Mosque (at Mecca). 9:93:608. They argue that it was a mode of revelation for the Prophet in symbolic form for the guidance of the Muslim nation. This event also foretold Muslims that God would now raise Muslims up as a superpower and Jerusalem would soon fall into their hands, which happened indeed within less than three decades of this event.
"Third holiest site"
Regarding "The Three Virtuous Mosques in Islam", the authentic Islamic creed regarding the 'holiness' of any place is mentioned by the Prophet Muhammad himself in many hadiths. Al-Bukhari reported in his authentic Collection of hadiths (i.e. Sahih al-Bukhari) that the Prophet (peace be upon him) said, "The rihaal must not be fixed (i.e. to go any where) [rihaal means 'luggage and provision a traveler usually takes with him in a long journey] except to three mosques: al-Masjid al-Haram (in Makkah), the Messenger's mosque (in Madinah) and al-Aqsa mosque (in Jerusalem). " (No.1189)
In this hadith, the Prophet prohibits Muslims from traveling to any mosque to visit (as a holy site) and to get reward for it except to the three mentioned mosques. No mosque carries special virtues other than the three mosques, that is probably due to their origin and who built them. We know that all of these mosques were built by God's Messengers (Ibrahim, Ya'qub and Muhammad). Once Abu Dharr asked the Prophet, "O Allah's Apostle! Which mosque was built first?" He replied, "Al-masjid-ul-Haram." I asked, "Which (was built) next?" He replied, "Al-masjid-ul-Aqsa." I asked, "What was the period in between them?" He replied, "Forty (years)." He then added, "Wherever the time for the prayer comes upon you, perform the prayer, for all the earth is a place of worshipping for you." (Sahih al-Bukhari, no. 3194) All other masjids that were built after the Prophet's mosque in Madinah are therefore the same in virtue and they don't carry any special status in Islam unless the Prophet (peace be upon him) had said so, regardless who built the mosque or what exist in inside it.
Throughout the history, humans built structures and claim that they are holy with out giving any evidence of their "holiness". In Islam, the "holy" place is the place that Allah and His Messenger made holy, not what people claim to be so.