Epidemiological studies require characterisation of pathogenic yeasts at and below the species level. The chromosomes of 130 strains of four pathogenic species of the genus Candida, isolated from clinical material, were separated by pulsed field electrophoresis with the clamped homogeneous electric field (CHEF) technique. Each species was characterised by a distinct electrophoretic karyotype (EK). Furthermore, smaller variations of the EK amongst strains belonging to the same species appeared to offer a useful means of strain differentiation. A karyotyping system is proposed for C. albicans. The EKs were assigned to a code of four numbers which designated the number of bands that could be resolved in each of four sets of chromosomes. Morphotypes of the colonies of C. albicans on malt agar plates, which did not correlate with the EK, could provide a complementary means of strain characterisation in epidemiological studies.