Palygorskite has been reported in alluvial sediments and in soil clays in Central Iran, but it is not known if it is inherited or formed in situ. Here, we sampled Calcids developed from Triassic and Cambrian dolomitic formations in the southwestern part of Yazd and performed soil and clay characterization by X-ray diffraction and fluorescence, optical and scanning electron microscopy and energy dispersive X-ray spectrometer analyses. Our results suggested palygorskite neoformation in the calcic soil horizons in Calcids. The soils with aridic soil moisture regime and high Mg concentration, during the formation of a calcic horizon by precipitation of secondary calcite, conditions were suitable for authigenic palygorskite crystals of long size (>10–20 μm) and their stability. In addition, the occurrence of short-size (about 2 μm) palygorskite fibers in the lower gypsic horizon probably resulted from its translocation from the upper horizons. Therefore, such results suggested palygorskite neoformation in the calcic soil horizons in these Calcids of Iran.