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This study assessed genital shedding of HIV in patients on intermittent combination antiretroviral therapy (cART) and assessed predictors of having detectable genital HIV RNA in 156 Thai patients with CD4 > 350 cells/?L and HIV RNA <=50 copies/mL who were randomized to continuous therapy (CT, n = 65) or CD4-guided cART (n = 91). There were 383 matched genital and plasma HIV RNA samples (CT: 158, CD4 guided: 225). In 14 samples collected within eight weeks of treatment interruption, detectable HIV RNA was present in 29% of genital samples and 71% of plasma samples. In 55 samples collected after eight weeks of treatment interruption, detectable HIV RNA was present in 60% of genital samples and 98% of plasma samples. In 110 samples collected up to 96 weeks after treatment re-initiation, detectable genital HIV RNA was found in 8% of samples and all of these were within the first 17 weeks. Independent predictors of detectable genital HIV RNA were increasing age and increasing concentrations of HIV RNA in plasma. These findings support the role of cART in maintaining undetectable HIV RNA in genital secretions.