BACKGROUND: We conducted a clinic-based cross-sectional survey among 710 people living with HIV/AIDS in stable 'sexual' relationships in central and southwestern Uganda. Although sexual function is rarely discussed due to the private nature of sexual life. Yet, sexual problems may predispose to negative health and social outcomes including marital conflict. Among individuals living with HIV/AIDS, sexual function and dysfunction have hardly been studied especially in sub-Saharan Africa. In this study, we aimed to determine the nature, prevalence and factors associated with sexual dysfunction (SD) among people living with HIV/AIDS (PLWHA) in Uganda. METHODS: We conducted a clinic based cross sectional survey among 710 PLWHA in stable 'sexual' relationships in central region and southwestern Uganda. We collected data on socio-demographic characteristics (age, highest educational attainment, religion, food security, employment, income level, marital status and socio-economic status); psychiatric problems (major depressive disorder, suicidality and HIV-related neurocognitive impairment); psychosocial factors (maladaptive coping styles, negative life events, social support, resilience, HIV stigma); and clinical factors (CD4 counts, body weight, height, HIV clinical stage, treatment adherence). RESULTS: Sexual dysfunction (SD) was more prevalent in women (38.7%) than men (17.6%) and majority (89.3% of men and 66.3% of women) did not seek help for the SD. Among men, being of a religion other than Christianity was significantly associated with SD (OR = 5.30, 95%CI 1.60-17.51, p = 0.006). Among women, older age (> 45 years) (OR = 2.96, 95%CI 1.82-4.79, p<0.01), being widowed (OR = 1.80, 95%CI 1.03-3.12, p = 0.051) or being separated from the spouse (OR = 1.69, 95% CI 1.09-2.59, p = 0.051) were significantly associated with SD. Depressive symptoms were significantly associated with SD in both men (OR = 0.27, 95%CI 0.74-0.99) and women (OR = 1.61, 95%CI 1.04-2.48, p = 0.032). In women, high CD4 count (OR = 1.42, 95% CI 1-2.01, p = 0.05) was associated with SD. CONCLUSION: Sexual dysfunction has considerable prevalence among PLWHA in Uganda. It is associated with socio-demographic, psychiatric and clinical illness factors. To further improve the quality of life of PLWHA, they should be screened for sexual dysfunction as part of routine assessment.