<p><strong>Background:</strong> Sexual expression affects physical, mental and social well-being. There is a lack of understanding on sexual problems among patients on antiretroviral treatment in Africa. <strong></strong></p><p><strong>Methods: </strong>Using systematic sampling, HIV-positive patients were selected prior to commencing on ART from outpatient departments from three hospitals and followed-up for 20 months (n=495) and interviewed with a questionnaire.</p><p><strong>Results:</strong> Rates of self-reported sexual problems were high (34.3%, among men: 30.3% and women 36.0%) but significantly reduced from prior to ART (57.7%) to 20 months on ART (34.3%) (P=0.006). In multivariate analysis not being formally employed (odds ratio: 0.4, 0.2-0.9), having had sexual intercourse in the past 3 months (OR: 5.8, 1.7-19.8), taking medications for HIV-related opportunistic infections (OR: 2.5, 1.1-5.7), internalized stigma (OR: 1.4, 1.2-1.6), lack of social support (OR: 0.4, 0.3-0.6), and low depressive symptoms (OR: 0.9, 0.8-1.0) were found to be associated with sexual problems.</p><p><strong>Conclusions:</strong> This prospective study with a large sample of persons on ART showed evidence of reduction of sexual problems over time and a number of factors influencing sexual problems which should be addressed in health care provider interventions.</p>