The large circular leather pendants of 7.5 m diameter suspended from the walls at the gallery level and the inscription inside the central cupola are reminders of the fact that the building was also used as a mosque. The arabic inscriptions on the pendants as well as the cupola, done in the 19th century by the greatest artists of that day, are among the best examples of all times of this branch of art.
The mihrab (prayer niche) and the mimber (pulpit) inside the apse of the church, as well as the chanters' balcony are later additions. On the other hand, the square shaped area marked by pieces of coloured marble just in front of the chanters balcony was probably from the 12th century, marking the place where the emperors were to stand while being crowned.

Mosaic mural at the end of the southern gallery: Virgin Mary and infant Jesus, 12th century Emperor John ll Comenius, Empress Irene. At the sidewall of this mural, the sick price Alexios is seen. The roll presented represents donations to the church, and the leather bag represents gifts of gold. The recial characteristics of the Hungarian-born empress may be observed clearly in the mural.
On the two sides of the nave stand two large urns. These urns are of antique origin and were brought in from the ancient city of Pergamum during the late 16th century. At the northern corner of the nave stands the Perspiring Column surrounded at the lower part by a bronze belt. The column has a finger-hole on its body and a lot of myth going for it.
Of the buttresses that support the structure, the one at the north has a ramp inside which provides for easy ascent to the upper galleries. The magnificent view of the nave is especially impressive from these galleries that surround the building at three sides. During the days of the Byzantine Empire, parts of these galleries were reserved for the ladies of the court and other parts were used for church congregations. On the wall of the northern gallery there is a single mosaic mural while the wall of the southern gallery is adorned with other murals, each depicting three holy personalities.
The large mosaic panel seen while leaving the museum through the interior narthex is a work of art from the 10th century. The central figure in this panel with a distorted perspective is the Virgin Mary with the infant Jesus on her knees. To her sides are Emperor Constantine the Great presenting them with the city walls he has built and Emperor Justinian presenting them with the Haghia Sophia. The colossal doors partly buried into the floor that are seen while exiting date back to the 2nd century B.C. and were brought from Tarsus, probably from a pagan temple there, and reused here.
In the courtyard of the museum are some structures of Turkish origin, built at different times. These are tombs of Sultans, a school, a clock-setting house and an ablution fountain. The minarets at the eastern side were added to the building in the 15th century and those at the west in the 16th century.
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