Geochemical well logs recorded in the Cajon Pass Scientific drillhole provide an estimate of the elemental concentrations of Si, Al, Fe, Ca, K, Th, Ti, S, and the HREE Gd. The continuous geochemical profiles were used to define a lithostratigraphy in the cystalline basement from 501 to 1,829 m. The interval between the faulted top of basement and a thrust fault at 689 m consists of six alternating slivers of granite and granodiorite. Interlayered granitic and granodioritic units were then encountered to another fault at 1290 m, whereas gneisses of granitic to tonalitic composition were logged in the basal portion of the hole. Linear discriminant analysis of major element chemistry, as well as variations in Gd, Th, Ti, and S, were used to demonstrate that each of the major lithostratigraphic units is chemically distinct. Different trace element signatures and variable degrees of metamorphism indicate a complex thermal and hydrological history for the basement rocks encountered in the Cajon Pass well.