OBJECTIVE: To examine if correlates of HIV-1 genital shedding in cross-sectional studies can be used to determine the risk of shedding in individual HIV-1-positive women. STUDY DESIGN: Longitudinal samples from blood and cervix were obtained from 18 HIV-1 infected women, and HIV-1 RNA and cell-associated DNA virus, and beta-chemokine levels, were measured. Associations between variables were analyzed at both individual and group level. RESULTS: The variation over time was 2.9-, 2.1-, and 2.3-fold in plasma RNA, PBMC DNA and cervical RNA load, respectively, and reached 6.2-fold in cervical DNA load. Differences were observed between associations in individual- and group-level comparisons, suggesting that a separate reservoir of HIV replication may exist in the genital tract of some women, which is influenced by local environmental factors. CONCLUSIONS: Our study underscores the importance of caution during contact with genital fluids at all stages of infection and disease regardless of treatment and HIV-1 blood loads.