Phase and antigenic variation are mechanisms used by microbial pathogens to stochastically change their cell surface composition. A related property, referred to as phenotypic switching, has been described for some pathogenic fungi. This phenomenon is best studied in Candida albicans, where switch phenotypes vary in morphology, physiology, and pathogenicity in experimental models. In this study, we report an application of a custom Affymetrix GeneChip representative of the entire C. albicans genome and assay the global expression profiles of white and opaque switch phenotypes of the WO-1 strain. Of 13,025 probe sets examined, 373 ORFs demonstrated a greater than twofold difference in expression level between switch phenotypes. Among these, 221 were expressed at a level higher in opaque cells than in white cells; conversely, 152 were more highly expressed in white cells. Affected genes represent functions as diverse as metabolism, adhesion, cell surface composition, stress response, signaling, mating type, and virulence. Approximately one-third of the differences between cell types are related to metabolic pathways, opaque cells expressing a transcriptional profile consistent with oxidative metabolism and white cells expressing a fermentative one. This bias was obtained regardless of carbon source, suggesting a connection between phenotypic switching and metabolic flexibility, where metabolic specialization of switch phenotypes enhances selection in relation to the nutrients available at different anatomical sites. These results extend our understanding of strategies used in microbial phase variation and pathogenesis and further characterize the unanticipated diversity of genes expressed in phenotypic switching.M any pathogenic bacteria, fungi, and protozoa have evolved strategies for alternative expression of surface-related phenotypes, a facility that enables their escape from immune surveillance and adaptation to changing environments. Antigenic variation, as displayed by African trypanosomes, Neisseria spp. and Borrelia spp., is a well studied example (1-4). Variation between phenotypes can be reversible and stochastic, leading to the expression of predefined traits which, when superimposed on classical environmentally responsive sensor mechanisms, extend the phenotypic diversity of the pathogen. In bacteria, many mechanisms have been described that lead to the expression of contingency loci that regulate expression of pili, flagella, adhesins, and surface-associated lipopolysaccharides and lipoproteins (5, 6).Strains of Candida albicans, the most important fungal pathogen of humans, are able to spontaneously and reversibly switch phenotypes at high frequency (7). Three different switching systems were first described by . C. albicans strain 3153A alternates between phenotypes distinguished by at least seven colony morphologies; conversion from the original smooth to other variant colony morphologies occurs at a combined frequency of 1.4 ϫ 10 Ϫ4 (11). Another system includes strains that switch between coloni...