The clay mineralogy of soils and of the main calcareous sedimentary parent rocks of southern Iran were investigated to determine their origin and factors controlling their distribution pattern in soils. The results revealed that the soil-available moisture plays the major role in the distribution pattern of palygorskite and smectite clay minerals in the arid and semi-arid areas studied. There is an inverse correlation between palygorskite and smectite with regard to the soil-available moisture as expressed by P/ET° (ratio of mean annual precipitation to mean annual reference crop evapotranspiration). At P/ET° values >0.4 palygorskite transforms to smectite. Smectite is thought to be mainly of ‘transformed’ origin. It is detected in trace amounts in soils of more arid areas and increases in soils having greater available moisture. The general decrease in illite content with depth is related mainly to its transformation to smectite under favourable moisture conditions of the deeper horizons. Palygorskite is considered to be inherited in plateau soils of the arid regions whereas in saline and alkaline soils and soils with high gypsum, it is mainly of authigenic origin. The P/ET° and gypsum content show a significant correlation with the palygorskite content. The occurrence of kaolinite in some soils is due to its inheritance from the surrounding kaolinite-bearing Cretaceous rocks. Illite and chlorite abundance in soils is also largely related to their presence in parent rocks. The rare occurrence of vermiculite in the studied calcareous soils is mainly related to its lower stability under high pH, low Al activity and the presence of large amounts of Si and Mg in soils.