Candida albicans and caries are frequently investigated among healthy and immunosuppressed individuals. The objective of this study was to demonstrate the presence of C. albicans on both oral soft and hard tissue and to investigate, at molecular level, the genetic subtype of the organism from the two oral sites. Tongue swabs and dentine scrapings from 362 HIV-positive children, referred for the extraction of carious primary teeth, were cultured on CHROMagar and identified to species level with ID32C. Histological staining of extracted carious teeth was also done. In patients with positive C. albicans cultures from both the tongue and carious dentine, DNA fingerprinting of such paired isolates was performed, using Southern blot hybridisation with the Ca3 probe. Yeasts were cultured from the tongue of 151 (41.7 %) individuals and 57 (37.7 %) simultaneously yielded positive C. albicans cultures from carious dentine. Nine different yeast spp. were identified from the tongue using the ID32C commercial system, but C. albicans was the only species recovered from carious dentine and histological investigation demonstrated fungal elements penetrated into the dentine and not limited to superficial debris on the floor of the cavity. Twelve of 13 paired isolates of C. albicans revealed identical fingerprinting patterns. The findings from this study demonstrated that in a particular individual, the same genetic subtype of C. albicans was capable of colonising both oral soft tissue and carious dentine. This renders carious teeth a constant source, or reservoir, of potentially infectious agents and, particularly among immunosuppressed individuals, should therefore not be left unattended.