Abstract Patients that undergo organ transplantation have a high risk of developing various malignancies, depending on the duration and magnitude of immunosuppressive therapy. Among others, a 10-fold increased relative risk has been reported for the development of anal cancer. There is a strong association between persistent infection with high-risk mucosal types of human papillomavirus (HPV) and anogenital neoplasia. In this study we analysed the prevalence of anal HPV infection in organ transplant patients before starting immunosuppressive therapy. In a university transplant unit, patients (n= 60, 40 male, 20 female) that were undergoing solid-organ transplantation (kidney, liver) for the first time were routinely screened for anal HPV infection. Anal swabs were obtained within 24 h after transplantation and analysed for the presence of mucosal-type HPV DNA by liquid DNA/RNA hybridization [hybrid capture (HC) 2 test]. Overall, some type of HPV DNA was detected in 14/60 (23.3%) patients; 9/60 (15%) were positive for high-risk HPV and 8/60 (13.4%) were positive for low-risk HPV, and 3/60 (5%) were positive for both types. Prevalence of HPV infection tended to be higher in patients that were receiving liver transplants than in those receiving kidney transplants (29.4% vs. 20.9%), but the difference did not reach statistical significance. In our series of organ transplant patients the prevalence of previous HPV infection (23.3%) before immunosuppressive therapy was started was higher than that found in previous epidemiological studies or in a control group. In particular, there was a high rate (15%) of infection with oncogenic HPV types. These findings have important implications on screening and surveillance policies in this patient group at risk of developing neoplasias, including anal cancer.