Introduction: Our study provides data on the prevalence of human papillomavirus (HPV) related disease and vaccination rates among users of pre-exposure prophylaxis (PrEP) in a primary care clinic. Results highlight an opportunity to partner HIV and HPV prevention efforts. Methods: This is a retrospective chart review of PrEP patients in an urban Midwestern Family Medicine clinic. We conducted univariate analyses for HPV vaccination status and the prevalence of any HPV-related disease. We then examined bivariate relationships between vaccination status and insurance coverage, provider type, and age. Results: Of all 78 PrEP patients identified, 21.8% (n = 17) were vaccinated. Of the 59 patients 45 years or younger, 28.8% (n = 17) were vaccinated. There was no association between insurance or provider type and vaccination status. Patients 26 years or younger were 3 times more likely to be vaccinated than those ages 27 to 45 (56.3% vs 18.6%, P = .0011). Three unvaccinated patients had HPV-related disease. Conclusions: Despite ongoing risk of HPV infection and frequent interaction with the medical system, this study found most PrEP users continue to be unvaccinated. This is a significant missed opportunity for HPV prevention. With the FDA approval of the HPV vaccine for individuals age 9 to 45, PrEP patients in this age range would benefit from clinicians partnering HPV vaccination with PrEP prescribing.