The eastern flanks of Mount Elgon, an early Miocene stratovolcano, host caves (∼150 m long, ∼60 m wide, ∼10 m high) of debatable origin. Many animals, primarily elephants, “mine” the pyroclastic bedrock for sodium-rich salts. Speleogenesis has been argued to be primarily zoogeomorphic, or primarily dissolutional with only minor zoogeomorphic modification. This report provides the first detailed mapping and geomorphological study of the caves. Speleogenesis is polygenetic and strongly related to lithology. Geological units are, from the top down, ∼2 m of dense pyroclastic agglomerate cap rock over which water falls, ∼10 m of more permeable agglomerate, up to ∼0.2 m of discontinuous impermeable lava, ∼2 m of very soft and permeable agglomerate, and >2 m of impermeable swelling-clay tuff. Caves develop behind waterfalls under surface stream valleys by sapping of the incompetent agglomerate above the clay, and failure of the clay (aquiclude and base level for speleogenesis), followed by collapse of harder agglomerate layers above. The dominant passage shape is breakdown dome, with abundant fresh collapse. Geophagy by elephants and other species, and human mining significantly modify and enlarge the caves and remove collapse debris. These activities, focused on accessible and salt-rich units, create quasi-horizontal undercuts (up to ∼4 m tall and deep), the loci of which move upward as collapse raises the floor. Significant erosion also occurs by incongruent dissolution, corrosion, pressure release, efflorescence flaking, and biogeochemical activity from huge bat colonies. No evidence was found of channeled flow, or of phreatic or vadose activity. These caves are probably no older than Holocene.