Nodular, pisolitic, and plastic kaolins from Kalabsha area, Egypt were investigated for their textural, mineralogical, and geochemical compositions to examine their source and origin. The three kaolins are composed of kaolinite, quartz, anatase, and traces of hematite and rutile. Clay fractions have relatively high Nb (56–189 ppm) and Zr (480–1260 ppm) contents. Heavy minerals from the sand fractions are composed of zircon, high Cr rutile, and leucoxene. Detrital quartz occurs as either monocrystalline or polycrystalline grains with worm-like corrosion features. Two types of quartz were distinguished based on their cathodoluminescence (CL) analysis; bright and dark luminescence quartz. Rare earth elements (REEs) patterns show enrichment of light REEs relative to heavy REEs ((La/Yb) N = 1.6–10) and negative Eu anomaly (Eu*/Eu = 0.6–0.7). Nodular and pisolitic kaolins show distinct positive Ce anomaly (Ce*/Ce = 1.2–3.4) and a variable LREE depletion. The pisolitic kaolin is considered here as flint kaolin based on its unique characteristics such as hardness, massiveness, conchoidal fracture, high density, very fine-grained nature, resistance to slacking in water, high crystallinity, and homogeneous compositions. Abundance of high Cr rutile, polycrystalline, and dark luminescent quartz suggest a contribution of medium to high grade metamorphic mafic rocks to the source of Kalabsha kaolins, while presence of zircon, bright luminescence monocrystalline quartz, and REEs pattern indicate a contribution of granitic rocks. The unusual high Nb contents attest to a contribution of alkaline rocks in the source area of the deposits. Lithostratigraphic succession, pisolitic texture, corroded quartz, depletion of many trace elements including LREE, distinct positive Ce anomaly, unusual grain size distribution, and compositional homogeneity suggest a lateritic precursor of the pisolitic flint kaolin. The lateritic precursor sediments have been deferrated and resilicified in the sedimentary basin to form the whitish flint clays with their unique physical and mineralogical characteristics as a result of volume increase associated to the transformation of Al-hydroxide minerals to kaolinite. Textural and geochemical variations unambiguously show that the overlying plastic clays are not derived by reworking from the pisolitic kaolins, but are derived from the saprolites underlying the lateritic crusts in the source region (sequential stripping).