Al-Azhar is one of the oldest mosques in historic Cairo. It was constructed by the Fatimids between 970-972 AD Most of historic Cairo buildings included Al-azhar are made mainly of carbonate stones that belong to Eocene Mokattam formation. These carbonate stones exhibit considerable damage related in many cases to the salt crystallization. Mineralogical investigation revealed that the studied samples can be classified as pure limestone to dolomitic limestone. The samples extracted from deteriorated surfaces showed clearly the crystallization of gypsum and halite filling the pores of stone material when they examined by Scanning Electron Microscope (SEM). These observations were confirmed by the means of Ion Chromatography (IC) analysis which in some samples the accumulations of chloride, sulphates and nitrates were high compared with the quarry samples. The strength of sample extracted from a surface where the salts occurred as subflorescence was showing a significant reduction by almost 42% while where salts occurred as efflorescence, the strength of the extracted cores showed slight reduction.