The pattern of candidal colonisation was studied in a group of terminally ill patients receiving antifungal treatment for oral candidosis. A total of 43 isolates of C. albicans was collected pre- and post-antifungal treatment from patients up to a maximum period of 4 weeks. Isolates were analysed by electrophoretic karyotyping (EK) and by inter-repeat polymerase chain reaction (IR-PCR). Fifteen electrophoretic karyotypes and 17 IR-PCR profiles were identified. Sequential isolates from 10 patients yielded identical profiles in both EKs and IR-PCR analyses. In the case of four patients, minor differences in the profiles were obtained by either EK or IR-PCR. The findings suggest that antifungal treatment in this patient group fails to eradicate the original C. albicans strain, thereby allowing recolonisation of the oral cavity. The present study has also shown that either EK or IR-PCR is a useful typing approach in such epidemiological investigations.