Immunomagnetic separation (IMS) was utilized for the selective isolation of Cryptococcus neoformans from environmental sources, such as soils and pigeon droppings. Magnetic beads coated with anti-cryptococcal IgG (serotypes A and B) were used to isolate the fungus. In a modeled spiking experiment using C. neoformans serotype A strain and anti-serotype A antibody, the recovery rate of the cells was more than 47%. Specificity experiments using C. neoformans and Candida albicans showed that the beads, when coated with specific antibody for C. neoformans, were highly effective for the separation of C. neoformans strains from C. albicans (more than 97%). The IMS of serotype B cells with purified anti-serotype B antibody indicated a high specificity. When this IMS technique was applied to soils and pigeon droppings, C. neoformans cells were selectively isolated from 3 out of 8 samples, and C. neoformans DNAs were identified by PCR. Therefore C. neoformans cells were thus selectively isolated and the efficiency of the technique further confirmed.