The defile of the Khyber Pass is cut in the massive gray recrystallized Khyber Limestone whose thickness exceeds 3,000 feet. Although no fossils have been found in the immediate vicinity of the pass, assemblages collected at the end of the last century from 5 miles south of the pass, and recently collected fossils from Afghanistan, suggest strongly that the limestone is Carboniferous to Permian and perhaps Jurassic in age. The basal contact of the Khyber Limestone in places appears to be conformable upon the quartzites and tuffs of the Ali Masjid Formation; elsewhere it is probably an unconformity or a fault, especially where the limestone lies directly on the Ordovician to Carboniferous Landi Kotal Slate. The Ali Masjid Formation overlies the Shagai Limestone, which, in turn, rests in fault contact on the Landi Kotal Slate.
Structurally the area is characterized by at least four major, roughly east-west trending thrust or reverse faults, along which relatively older rocks have moved southward over younger rocks. A north-northeast-trending system of alternating anticlines and synclines has been superimposed on the earlier structures. Elevated terraces and alluvial valleys suggest a very recent uplift of about 600 to 1,000 feet.