The clay fractions of saprolites from granites, basalt, and schists in Egypt were subjected to mineralogical and geochemical investigations to examine the effect of source rock on the composition of the saprolites and the possibilities of these saprolites as a source of the nearby sedimentary kaolin deposits. The clay fractions of the studied saprolites show mineralogical and geochemical variations. Saprolites from the granites consist of kaolinite, while saprolites from the basalts are composed entirely of smectite. Schists-derived saprolites are composed of kaolinite in some cases and of a mixture of kaolinite, illite, and chlorite in the other. Saprolite from the basalt is characterized by relatively higher contents of TiO2 and Ni compared to the saprolites from granites. Saprolites from granites have higher contents of Ba, Li, Pb, Sr, Th, Y, and Zr compared to those of the saprolites from the basalts and schists. Saprolites from different schists show variations in the distributions of many constituents, such as TiO2, Cr, Ni, Ba, Y, and Zr. Although chondrite-normalized rare earth elements (REE) patterns are characterized by relative enrichments in the light rare earth elements (LREE) compared to the heavy rare earth elements (HREE) in all saprolites, granitic saprolites show negative Eu anomalies, while saprolite from basalt has no Eu anomaly. REE patterns of the saprolites from schists exhibit slight positive Ce anomalies and slight to moderate negative Eu anomalies. Weathering of saprolites from the basalt and metasediments is classified as the bisiallitization type, while weathering of saprolite from the granite is allitization type. Saprolites from schists vary from the bisiallitization (Aswan and Abu Natash) and allitization (Khaboba) types. Saprolites from the Khaboba schist can be considered the possible source of the Carboniferous kaolin deposits in the Hasber and Khaboba areas of Sinai, based on the similarity in the mineralogy and geochemistry of major, trace, and REE between the saprolites and the deposits. On the other hand, Carboniferous sedimentary kaolin deposits in the Abu Natash area, as well as the Cretaceous kaolin deposits in all areas of Sinai, might have been derived from the nearby schist saprolites, based on the similarity in the mineralogy and geochemistry between the saprolites and the kaolin deposits. Granites from the Arabian-Nubian Shield (ANS) and East Sahara Craton (ESC) are the possible sources of the pisolitic and plastic kaolin deposits in the Kalabsha area (Aswan), as indicated by the similarity in the mineralogy and geochemistry of the granitic saprolites and the kaolin deposits.