Vulvar/vaginal human papillomavirus (HPV) infections may precede cervical infections, and certain low-risk types may display vaginal tropism. We evaluated whether incident infections in young women display site-specific preferences by HPV risk group or phylogenetic species. Although incident infections were more likely to be detected in the vulva/vagina than in the cervix (odds ratio, 4.38 [95% confidence interval, 2.51-7.63]), the majority were first detected at both sites. Low- or undetermined-risk types were more likely than high-risk types to be first detected in the vulva/vagina (P = .03). Site-by-species differences were not statistically significant. Our results suggest that low- or undetermined-risk HPV types preferentially infect vaginal epithelium.