Candida albicans oral strains collected from caries-free and caries-active healthy children ranging from 24 to 36 months old, were studied. The aim of the study was to determine proteinase and phospholipase activities produced by Candida albicans in the two groups and to determine the phenotypic diversity of these enzymes based on genetic polymorphism using the AP-PCR method. Strains identified by morphological and fermentation tests as C. albicans were grown in proteinase and phospholipase agar media at 37ºC for 7 and 4 days, respectively. After the incubation period, the enzyme activity of the proteinase and phospholipase positive strains was measured. All strains were subjected to AP-PCR, using the arbitrary primer AP-3. The enzymatic analysis showed no differences between the two groups. The AP-PCR method was effective in demonstrating intra-individual genetic polymorphism in C. albicans, showing a greater clonal diversity in caries-active versus caries-free children. Dendograms of similarity showed only intra-individual clonal lineage. The results suggest that the enzymatic profile does not depend on the genotypic characteristics of the strains.