Extensive surface alterations of rock-cut churches such as color change, exfoliation, and granular disintegration have been examined starting with the surface down to about 10 centimeters depth. Mineralogical and petrographic examination have been done by x-ray powder diffraction analysis, optical microscopy, and scanning electron microscopy coupled with EDAX. Soluble salt content has been determined by using spectrophotometric methods as well as pH and conductivity measurements. Restricted microclimatic investigations have been performed by taking temperature and humidity measurements of the surfaces and the atmosphere in winter and early summer. The results have been interpreted in terms of the types of alteration, the depth of alteration, and possible methods of conservation.