Twenty-five caves of speleological and palaeontological interest were investigated for the presence of Cryptococcus spp. within the Apulia region of Italy. Five hundred and forty-five specimens of soil, mud, animal faeces, water and decayed animal and plant remains were examined. Faecal specimens from bats, pigeons and foxes in three caves yielded Cryptococcus neoformans var. neoformans and C. laurentii, C. neoformans var. neoformans and C. albidus were isolated from two soil specimens. Only three caves were positive for the presence of C. neoformans, but the survey documents the finding of a possible natural reservoir in Apulia. It is the first record of occurrence of this yeast in association with cavernicolous habitats, and indicates the potential role of caves in exposing speleologists to life-threatening fungal infections.