A random sample of 960 women aged 15-59 years enrolled in a population-based study in rural Uganda were asked to provide self-collected vaginal swabs for human papillomavirus (HPV) testing by hybrid capture assay. The intensity of HPV infection was assessed by the relative light unit (RLU) ratio in the specimen-to-positive control (PC) ratio. In total, 898 women (93%) provided a swab and 737 provided serum for human immunodeficiency virus type 1 (HIV-1) determination. HPV prevalence was 16.7% and was highest in younger women. HIV-1 prevalence was 17.8%. HPV prevalence was 44.3% in HIV-positive and 10.2% in HIV-negative women (rate ratio, 5.36; 95% confidence interval, 3.81-7.54). The intensity of HPV infection was significantly greater among HIV-positive than HIV-negative women (54. 4 vs. 11.1 RLU/PC; P=.026); intensity of infection was highest in women aged <30 years. The higher prevalence and intensity of HPV infection in HIV-positive women could facilitate HPV transmission in this population. Self-collected vaginal swabs could be used in population-based screening to identify women at high risk of cervical neoplasia.