Al-Aqsa is part of 180,000 square yard compound of al-Haram el-Sharif, or the Noble Sanctuary (or Sacred Precinct), occupying one-sixth of the walled area of the Old City of Jerusalem (currently occupied by Israel). The area, directly behind the Wailing Wall (itself by Jews considered a remnant of the Temple of Solomon but by Muslims considered part of al-Aqsa), can accommodate hundreds of thousands of worshipers.
The compound has been central to nearly a century of conflict between Jews and Muslims in the region as both sides have battled over access rights, ownership, historical meaning and even spiritual value. The first major Jewish-Arab riots, in 1929, were sparked by conflict over access rights to Haram el Sharif. Muslims since 1948 have feared that Israeli Jews intend to destroy Al Aqsa in order to build another temple there.
When Jordan took control of Old Jerusalem in 1948, it barred Jews' access to the Temple Mount. After Israel occupied the Old City in 1967, it restored access and did not prevent Muslims from worshiping there. Conspiracy theories, however, abound.
History and Architecture
Al-Aqsa, which means the farthest, is the second-oldest mosque after the Kaaba. It is believed to be on the site of a rock revered by Jews as the foundation stone and axis of the world, and where the Prophet Muhammad prayed. The prophet prayed at the rock, if not to the rock, during what has been rendered as a miraculous night journey he undertook on a white flying horse (l-Buraq El-Sharif) from Mecca to Jerusalem about 10 years after he began receiving "revelations" that disciples later codified as the Koran. The legendary rock is today covered by a golden dome, the Dome of the Rock. Muhammad instructed his followers to pay their respects to "the farthest mosque" (hence, al-Aaqsa), and for almost two years after his journey to Mecca, Muslims prayed facing not Mecca, but Jerusalem.
Artistically and architecturally more ancient and important than the Kaaba, the Dome of the Rock was built in 691 by Caliph Abdel Malik. It does not conform to the plan of a typical mosque. It is octagonal, with an inner colonnade, and was originally built with somewhat subversive, if not apostate, intent--to rival Mecca and draw more pilgrims. The architecture of al-Aqsa was significantly influenced by the Christian churches of Jerusalem.
The mosque was set on fire by Michael Dennis Rohan, an Australian fundamentalist Christian, on Aug. 21, 1969. The mosque remains at the heart of Palestinian-Israeli tensions.

