The mosque which he completed, the El-Hakim is the second largest Fatimid mosque in Cairo. The mosque was started in 990 by the Caliph Al Aziz Billah son of the famous Khalifa Al Moez Lideen Allah Al Fatimy, and was completed by al-Hakim bi-Amr Allah and his overseer Abu Muhammad al-Hafiz 'Abd al-Ghani ibn Sa'id al-Misri in 1013. 

To secure serenity and solemnity during the Fatimid Era, wood cutters with their camels, mules and carts loaded with straw and wood logs were banned from treading the street which was lit all night by lanterns hung on the facades of buildings and shops. 

Over its lifetime, the building has served as a prison for captive Crusaders (though we have also been told of it being used as a church by them as well), Napoleon's warehouse, Salah al-Din's stable, a lamp factory, and a boys' elementary school under Nasser, when a basketball court was marked off in the courtyard. Napoleon's soldiers at the end of the 18th century left the mosque in a bad state and it fell into disrepair. It was later revived during the reign of Khedive Tawfik as the foundation for the first Islamic Museum before that museum was relocated to Bab al-Khalq in 1903. Prior to the modern era, the last time it was mentioned as being used as a mosque was in 1452 AD. 

Originally the mosque stood outside the enclosure walls of Fatmid Cairo until Badr al-Gamali rebuilt the Northern Wall to include the al-Hakim mosque within the boundaries of the enclosed city. 

This is a good example of a congregational mosque that was typical to early Islamic architecture. The mosque is constructed of brick with stone facades and minarets, and covers about the same area as the Ibn Tulun Mosque. It has an  irregular rectangular plan with a rectangular, central, open courtyard surrounded by arcades supported by compound piers, with a prayer hall whose arcades are also carried on compound piers. The front facade on the north was given a central projecting monumental portal. The mosque has three domes and a central nave in the qibla prayer hall, higher and wider than the lateral aisles, with a basilican disposition.  The termination of this aisle at the mihrab is marked by a dome carried on squinches, and domes mark the outer corners of the prayer hall as well. 

Its two corner minarets, different in shape and decoration, were encased in projecting trapezoidal stone structures that project into the street, during the reign of el-Hakim in 1002-3 AD (though some have placed the dates of the encasing structures to 1010 AD). 

These minarets are the oldest surviving minarets in Cairo as they stand at the outer walls of the mosque. The bases are original and can be seen inside the buttresses, though the tops were replaced in 1303 by Baybars II al-Gashankir during the Mumluk period after an earthquake destroyed the upper stories.

Baybars was also responsible for the mabkhara finials, as well as the polychrome marble faced mihrab in the qibla wall to the right of the main mihrab. An interior staircase leads to the city's ramparts and a rampart walk that date from the 12th century. 

Given the strong affiliation of the Fatimids to North Africa and particularly to Qairawan in Tunisia, al-Hakim built his mosque in the tradition of the Great Mosque of Qairawan. However, it may also be said that the mosque was modeled after that of Ibn Tulun though the  clerestoried mihrab nave follows the style of the Mosque of al-Azhar. 

Very little of the original decorations remains after a restoration by an Ismaili Shi-i sect. The mosque has been encased in marble and only the wooden tie-beams, stucco carvings in the clerestory and in the Quranic inscriptions remain of the original decorations. 

Today, every Friday the mosque hosts hordes of worshippers who head for it weekly to perform their midday prayers, and to give Al Hakim mosque its fame as the most crowded mosque of Old Cairo. 

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