Calcareous and gypsiferous soils and major sedimentary rocks of Kohgilouye Boyerahmad province, Southwestern Iran, were investigated in order to determine the origin and distribution of clay minerals in soils of different climatic regions. The elevation of the Province varies from 500 m above sea level in southwest to 4409 m above sea level in northeast of the province. Precipitation ranges from about 330 mm in southwest to 1185 mm in southeast of the province. Mean annual temperature ranges from 10.5° C in southeast to 23° C in south west of the Province. This province is a part of the Zagros orogenic area and consists of carbonatic and gypsiferous alluvium derived from of Cretaceous to Quaternary rocks. According to Soil Moisture and Temperature Regime Map of Iran the soils comprise xeric, ustic and aridic-ustic soil moisture regimes along with mesic, thermic and hyperthemic temperature regimes. X-ray diffraction, transmission electron microscopy, scanning electron microscopy and physico-chemical studies were performed on the 12 major sedimentary rocks and soils of 37 pedons. Kaolinite, smectite, chlorite, illite, palygorskite and illite-smectite interstratified minerals were detected in the rocks studied. These clay minerals as well as vermiculite were detected in the soil studied. The results revealed that inheritance from the parent rocks is the main pathway for the occurrence of illite, chlorite, kaolinite and interstratified minerals in the soils studied. Although, pedogenesis of illite at soil surface of more humid regions has less importance. Larger amount of illite at soil surface of these regions supports this hypothesis. Kaolinite is present in Cretaceous sedimentary rocks and more prevalent in the Lower than Upper Cretaceous. Larger content of kaolinite was noticed in soils located on Cretaceous sediments. Climatic condition of the region cannot provide a favorable environment for the pedogenic formation of kaolinite. Although detrital input of this clay mineral is probable. Neoformation and inheritance are the main pathways for the occurrence of smectite in the studied soils. Simple transformation of illite to smectite may play a major role in decreasing illite content at soil surface. Climatic condition in the study area can provide a leaching environment for the release of K+ from micaeous minerals and mainly illite. Sub surface horizons of more humid soils showed larger amount of smectite possibly due to fine clay illuviation as well as inheritance from parent material. In contrast with more humid soils, lower humid soils exhibited larger amount of vermiculite at soil surface. Sensitivity of this clay mineral to weathering and transformation to vermiculite possibly is a reason for this distribution. Expansion of smectite after glycerol treatment was larger at soil surface as well as in soils of more humid regions. It may be in accordance with more decrease in smectite layer charge in the studied soils. Annual precipitation has an important effect on distribution of palygorskite in the soils studied. Larger content of this mineral was noticed in soils of the regions with the annual precipitation less than 400 mm. X-ray diffraction results revealed that palygorskite probably is transformed to smectite in more humid regions. Neoformation of palygorskite as a result of calcite and gypsum precipitation seems to be a major pathway for the occurrence of this mineral. SEM observations support this hypothesis. TEM studies revealed different morphological forms of palygorskite in relation to degree of weathering. Longer fibers with sharper tips of palygorskite were noticed in soils with lower degree of weathering.