The application of methods of Candida albicans DNA fragment length polymorphism analysis to correlations with phenotype and to questions in the epidemiology of Candida is shown. Twenty-nine different DNA types, in two broad classes, have thus far been demonstrated in 91 isolates. One type, IA2, was easily the most common (41% of isolates). A type is constant after multiple generations in vivo, as demonstrated in a mouse model. Isolates from individual medical centers were polymorphic, and DNA types were widely distributed geographically. Persons colonized with and/or having disease due to C. albicans at two or more body sites almost always had the same individual type. Sex partners studied had the same type in genital isolates. There was neither tight concordance nor random association of DNA type with previously described phenotypic groups. Likewise, some phenotypic characteristics were significantly associated with DNA type. Urogenital isolates were significantly associated with DNA type IA2. Colonizing and invading isolates included many different and overlapping DNA types. A cluster of cases in a hospital, previously reported to have been caused by a single organism (based on phenotypic studies), was shown to be due to multiple types. Phenotype switching, associated with transition from colonization to invasion, is suggested in these studies. The present series of studies demonstrates the application of DNA typing methods to classification and clinical problems.