Non-consensual sex is associated with HIV infection in Africa, but there is little longitudinal data on this association. We describe reported non-consensual sex among women over two decades in southwest Uganda, including associations with incident HIV infection. Between 1990 and 2008, individuals in a population cohort who recently seroconverted to HIV were enrolled into a clinical cohort, along with randomly selected HIV-negative controls. Participants were invited to the study clinic every 3 months, and females asked about recent experiences of sex against their will. Associations of non-consensual sex with HIV status were analyzed prospectively using conditional logistic regression, adjusting for age and year of interview, allowing for within-woman correlation. 476 women aged 14-81 enrolled and attended 10,475 visits over 19 years. The results show high levels of repeated non-consensual sex, often long after HIV infection. There was more reporting among women living with HIV compared to HIV-negative women (22 vs 9 %; OR = 2.29, 95 %CI 1.03-5.09), with the strongest associations among married participants. HIV programmes should address repeated sexual coercion before and subsequent to HIV infection.