The Hanging Church (El Muallaqa, Sitt Mariam, St Mary) derives its name from its location on top of the southern tower gate of the old Babylon fortress with its nave suspended above the passage. (Muallaqa translates to 'suspended') The church was first built, in Basilcan style, in the 3rd or 4th century. However, at that time it is unlikely that the church would have been constructed in this location. They covered the towers with palm trunks and a layer of stone. The main church is thought to have been built between the 5th and 6th centuries with the southeastern section called the "upper church" being added later. The church was destroyed in the 9th century. It was rebuilt in the 11th century and became the seat of the Coptic patriarchate until the 14th century.

It became known to travelers during the 14th and 15th centuries as the "staircase church" because of the twenty-nine steps that lead to the entrance.

The church is composed of a main court and two narrow suites separated by eight columns on each side. The court is further separated from the northern suite by a row of three columns with large ogee (arrow-shaped) arches. Columns separating suites were made of marble, except for one, which was made of black basalt. Columns, 23.5-m-long, 18.5-m-wide and 9.5-m-high, had corinthian-style capitals derived from earlier architectural styles.  

The church entrance lies south of the eastern wall of the front lobby, which is rendered at present into an open court, adorned with geometrical and floral plaster ornaments. Inside, there are seven sanctuaries in which six are in the two side aisles and one in the Church of St. Mark which is above. In front of the central sanctuary is a pulpit that dates from the 11th century and is supported by fifteen marble columns. On one of the bastions of the fortress is a chapel built for the Ethiopian saint Takla Haymanot. A wooden staircase leads up to this chapel. There are many objects that belong to the church inside the Coptic Museum. There are icons and manuscripts that can be seen there. Inside the church are collections of over one hundred icons of which the oldest dates from the 8th century. The craftsmanship of the iconostases in cedar, ebony and walnut and are inlaid with ivory and dates from the 10th to the 13th century is incredible.

On the eastern side of the church, there lie three altars dedicated to the names of the Virgin Mary (middle), St. John the Baptist (right) and St. Mar Guirguis (left). Facing these altars are wooden screens, of which the central, made of ebony inlaid with ivory, dates back to the 12th / 13th Century. The screen is stuffed with exquisite geometrical and cross-shaped patterns. The upper part shows icons depicting Christ as seated on a throne flanked by Virgin Mary, Arch Angel Gabriel and St. Peter on the right and John the Baptist, Arch Angel Michael and St. Paul (Boulos) on the left. The altar is covered with a wooden awning supported by four columns, with a seating platform for the clergy at the back. In addition to the Hanging Church, there is Abi-Sirga's Church, that lies some metres below street level. 

Adjoining, there are another six churches and a monastery, all of which lie on two rows separated by a corridor wide enough for the passage of a few persons.