Chronic vulvovaginitis due to Candida albicans is a major clinical problem for the physician. Although new antifungal drugs are now available, the therapeutic approach of this disease remains disappointing. The aims of this study were two-fold. First, we wanted to evaluate the reliability of a single sampling performed by most clinicians in verifying if the yeast infects the entire genital mucosa or a preferential site and, second, to biotype the strains recovered in order to see if more than one strain are responsible for the infection. We found, in 18 patients suffering from vaginal candidosis, that the entire genital mucosa was infected by the yeast and the strain recovered from the different genital sites in a single patient was the same in 100% of the cases. Only 1.4% of the samples were negative. In addition, we biotyped the strains obtained from the gastrointestinal tract of these patients to evaluate this site as a potential source of infection. We obtained gastrointestinal tract samples for 15 of the 18 patients and we could identify C. albicans in 100% of the cases. Furthermore, 73.3% of the patients harboured the same strains of C. albicans in the gastrointestinal tract as in the vagina.