Besides immunosuppression and UV radiation, human papillomavirus (HPV) infection was also suggested to be involved in the development of non-melanoma skin cancer, the most common malignancy after transplantation. In this study we used a comprehensive PCR assay to analyze the prevalence of individual HPV types in different skin lesions from transplant and non-transplant patients. HPV DNA was detected more frequently in squamous cell carcinomas (SCCs) of transplant recipients (75%) than the same lesion was in non-immunosuppressed patients (47%). Similar HPV prevalences were found in cutaneous warts (91% vs 94%), pre-malignant skin tumors (38% vs 36%), and normal skin specimens (17% vs 16%) of both patient populations. Overall, more than 40 different HPV types were identified. HPV types 5 and 8 were found more frequently in SCCs (26%) than in pre-cancerous (5%) or benign lesions (1%). All HPV 5- and HPV 8-positive SCCs were from immunosuppressed patients, indicating that infection with HPV 5 and HPV 8 may present an increased risk of SCC development in these patients.