Instigated by an increase in serious human Candida infections and aided by advances in technology, there has been renewed interest in the study of the epidemiology of fungal infections. Among the newer techniques available, contour-clamped homogeneous electric field (CHEF) electrophoresis has shown great promise as a tool for typing strains of Candida albicans. However, few studies have addressed the reproducibility of the preparatory and electrophoretic methods. Through a series of analyses on clinical isolates of C. albicans, we were able to demonstrate that (a) sample preparation induced no appreciable artifacts in CHEF banding patterns; (b) the electrophoretic patterns were reproducible over time; (c) changes in colony morphology were not associated with changes in the electrophoretic pattern, and (d) the method was more sensitive than restriction enzyme analysis (REA) for demonstrating strain differences. CHEF electrophoresis is a sensitive and reproducible tool for the study of Candida epidemiology. Further use and study of this methodology is warranted.