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To investigate self-administered vaginal swabs for assessing prevalence and correlates of carcinogenic human papillomavirus (HPV) infection in rural Rakai, Uganda.1003 sexually experienced women enrolled in a community cohort provided self-administered vaginal swabs collected at annual, home-based surveys. Carcinogenic HPV prevalence, adjusted odds ratios (AOR), 95% confidence intervals (CI) and associated risk factors were determined.Carcinogenic HPV prevalence was 19.2%: 46.6% among HIV positive and 14.8% among HIV negative women (p<0.001). Type-specific prevalence ranged from 2.0% (HPV 16 and 52) to 0.2% (HPV 31). Age-specific HPV prevalence decreased significantly (p<0.001) among HIV negative women; however, the decrease among HIV positive women was not as pronounced (p = 0.1). Factors independently associated with carcinogenic HPV infection were HIV (AOR 4.82, CI 3.10 to 7.53), age (AOR 4.97, 95% CI 2.19 to 11.26 for 15–19 year olds compared to 40+ years), more than two sex partners in the past year (AOR 2.21, CI 1.10 to 4.43) and self-reported herpes zoster, candidiasis or tuberculosis (AOR 4.52, CI 1.01 to 20.31). Married women were less likely to have prevalent carcinogenic HPV (AOR 0.46, CI 0.30 to 0.70).HPV prevalence and correlates measured using self-administered vaginal swabs were similar to studies that use cervical samples. Thus, self-collection can be used as a substitute for cervical specimens and provide an important tool for research in populations unwilling to undergo pelvic exam.