© 2018 Young et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background Intimate partner violence (IPV) is a significant global health problem. Women who experience IPV have increased HIV incidence, reduced antiretroviral adherence, and a lower likelihood of viral load suppression. There is a lack of evidence regarding how to effectively identify and support women living with HIV (WLWH) experiencing IPV, including uncertainty whether universal or targeted screening is most appropriate for lower-resourced settings. We examined physical and sexual IPV prevalence and correlates among WLWH in Uganda to understand the burden of IPV and factors that could help identify women at risk. Methods We utilized data from women receiving ART and enrolled in the Uganda AIDS Rural Treatment Outcomes (UARTO) cohort study between 2011 and 2015. Bloodwork and interviewer-administered questionnaires were completed every 4 months. IPV was assessed annually or with any new pregnancy. Multivariate models assessed independent socio-demographic and clinical factors correlated with IPV, at baseline and follow-up visits. Results 455 WLWH were included. Median age was 36 years, 43% were married, and median follow-up was 2.8 years. At baseline 131 women (29%) reported any experience of past or current IPV. In the adjusted models, being married was associated with a higher risk of baseline IPV (ARR 2.33, 95% CI 1.13–4.81) and follow-up IPV (ARR 2.43, 95% CI 1.33–4.45). Older age (ARR 0.96, 95% CI 0.94–0.99) and higher household asset index score (ARR 0.81, 95% CI 0.68–0.96) were associated with lower risk of IPV during follow-up. Conclusion There was a high prevalence of physical and sexual IPV amongst WLWH, and many women experienced both types of violence. These findings suggest the need for clinic-based screening for IPV. If universal screening is not feasible, correlates of having experienced IPV can inform targeted approaches.