DNA polymorphisms generated by the polymerase chain reaction (PCR) were used to differentiate clinical isolates of Candida. This PCR method employed single primers that were originally designed as hybridization probes for DNA fingerprinting experiments to probe minisatellite and microsatellite DNA sequences. To evaluate this procedure, 35 isolates from 20 patients in several intensive care units and 12 isolates obtained from the oral cavities of healthy dental patients were fingerprinted. The PCR-fingerprint patterns of isolates of Candida albicans from the immunocompromised patients revealed fewer differences than isolates from the dental service. Multiple isolates from different body sites of the same patients revealed that patients may harbour isolates of Candida with the same or different PCR-fingerprints. Since this method is generally simpler and faster than established methods of biotyping medically important yeasts, PCR-fingerprinting may prove useful for the surveying of large numbers of pathogens for epidemiological studies.