The opportunistic pathogen Candida albicans secretes aspartic proteinases (Saps), which raises a particular interest because of their role as virulence factors. Candida albicans possesses at least 10 members of a SAP gene family, all of which have been sequenced. Although the expression of the SAP genes has been extensively characterised under laboratory growth conditions and Saps contribute to the virulence of C. albicans in animal models of infection, few studies have analysed the difference of the in vivo expression of these proteinases in recurrent vulvovaginal candidiasis (RVVC), vulvovaginal candidiasis (VVC) and asymptomatic Candida carriers. The RT-PCR protocol was used to determine which of the SAP1 to SAP7 genes are expressed by C. albicans during asymptomatic Candida carriage, VVC and RVVC infection in this study. We found SAP2, the SAP4–6 and SAP7 were the predominant proteinase genes expressed in the sample of both Candida carriers and patients with VVC and RVVC. SAP2 and SAP4–6 mRNA were detected in all subjects. SAP1 and SAP3 transcripts were observed only in patients with VVC and RVVC. SAP7 mRNA expressions were detected in several of the patients and carriers samples. All seven SAP genes were simultaneously expressed in some patients with VVC and RVVC. This study demonstrates the differential expression of the secreted aspartic proteinases (Saps) genes during colonisation and VVC and RVVC infection in humans and correlates the expression of specific Candida species virulence genes with active disease and anatomical location.