High-risk genital human papillomavirus (HPV) infection is aetiologically linked to cervical cancer; however, data on the prevalence and determinants of high-risk HPV infection in Uganda are limited. We conducted a population-based cross-sectional survey among 18-49-year-old women in rural Southwest Uganda. The primary outcome was presence or absence of high-risk HPV DNA (for genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 or 68) in the genital secretions as determined by HPV DNA Hybrid Capture 2 assay (Digene Corp, Beltsville, MD, USA). In 314 women who participated, the prevalence of high-risk HPV was 17.2% (54/314; 95% confidence interval [CI]: 13-21). Older women had a lower proportion of high-risk HPV infection; with a 9% decrease in the odds ratio (OR) of high-risk HPV infection per year increase in age (OR = 0.91; 95% CI: 0.86, 0.96). The odds of detecting high-risk HPV infection was higher among women who were previously tested positive for HIV (OR = 12.1; 95% CI: 2.8, 52.3). In this population of rural Ugandan women, the prevalence of high-risk cervical HPV infection was high. Information on predictors of high-risk HPV infection and intention to receive a vaccine can guide future immunization initiatives for young sexually active women.