The polymorphism of a new microsatellite locus (CAI) was investigated in a total of 114 Candida albicans strains, including 73 independent clinical isolates, multiple isolates from the same patient, isolates from several episodes of recurrent vulvovaginal infections, and two reference strains. PCR genotyping was performed automatically, using a fluorescence-labeled primer, and in the 73 independent isolates, 26 alleles and 44 different genotypes were identified, resulting in a discriminatory power of 0.97. CAI was revealed to be species specific and showed a low mutation rate, since no amplification product was obtained when testing other pathogenic Candida species and no genotype differences were observed when testing over 300 generations. When applying this microsatellite to the identification of strains isolated from recurrent vulvovaginal infections in eight patients, it was found that 13 out of 15 episodes were due to the same strain. When multiple isolates, obtained from the same patient and plated simultaneously, were typed for CAI, the same genotype was found in each case, confirming that the infecting population was clonal. Moreover, the same genotype appeared in isolates from the rectum and the vagina, revealing that the former could be a reservoir of potentially pathogenic strains. This new microsatellite proves to be a valuable tool to differentiate C. albicans strains. Furthermore, when compared to other molecular genotyping techniques, CAI proved to be very simple, highly efficient, and reproducible, being suitable for low-quantity and very-degraded samples and for application in large-scale epidemiological studies.It is known that opportunistic yeast pathogens are common residents of the mucosal surfaces of the gastrointestinal tract, genitourinary system, and oral cavity in warm-blooded animals. Although several yeast species can be associated with infection, the predominant causal agent of candidiasis is Candida albicans. This yeast causes several infections in humans, including a wide variety of life-threatening conditions triggered by bloodstream infections, especially in immunocompromised patients. Since pathogenicity and antifungal susceptibility often vary among strains, a rapid and accurate identification of the disease-causing strains of C. albicans is crucial for clinical treatment and epidemiological studies.Advances in molecular biology in the last 2 decades have allowed the development of rapid molecular genotyping techniques for clinical and epidemiological analysis. Several molecular typing methods have been developed to differentiate C. albicans strains, including electrophoretic karyotyping (2), the use of species-specific probes such as Ca3 or 27A in restriction enzyme analysis (20,23,27,29,32,33,35), and PCR-based methods (1,10,21,24,28,37). More recently, short tandem repeats (STRs) or microsatellites have assumed increasing importance as molecular markers in fields so diverse as oncogenetics, population genetics, and strain identification and characterization. They occur in se...