Male circumcision (MC) reduces high-risk human papillomavirus (HR-HPV) infection in female partners. We evaluated the intensity of HR-HPV viral DNA load in HIV-negative, HR-HPV-positive female partners of circumcised and uncircumcised men. HIV-negative men and their female partners were enrolled in randomized trials of MC in Rakai, Uganda. Vaginal swabs were tested for HR-HPV genotypes by Roche HPV Linear Array which provides a semi-quantitative measure of HPV DNA by the intensity of genotype-specific bands (graded:1–4). We assessed the effects of MC on female HR-HPV DNA load by comparing high intensity linear array bands (3–4) to low intensity bands (1–2) using an intention-to-treat analysis. Prevalence risk ratios (PRR) of high intensity bands in partners of intervention versus control arm men were estimated using log-binomial regression with robust variance. The trial included 335 women with male partners in the intervention arm and 340 in the control arm. At enrollment, the frequency of HR-HPV high intensity linear array bands was similar in both study arms. At 24 months follow-up, the prevalence of high intensity bands among women with detectable HR-HPV was significantly lower in partners of intervention arm (42.7%) than control arm men (55.1%, PRR = 0.78, 95%CI 0.65–0.94,p= 0.02), primarily among incident HR-HPV infections (PRR = 0.66, 95% CI 0.50–0.87,p= 0.003), but not persistent infections (PRR = 1.02, 95% CI 0.83–1.24). Genotypes with high HR-HPV band intensity were more likely to persist (adjHR = 1.27 95% CI 1.07–1.50), irrespective of male partner circumcision status. MC reduces HR-HPV DNA load in newly infected female partners.