This study investigates human papillomavirus (HPV) infection in the oral cavities of 88 Australian renal transplant recipients and 88 immunocompetent controls. Oral cavities were examined for lesions and brushings collected for HPV analysis by consensus PCR. No warts were identified; HPV DNA was detected in 18% of transplant versus 1% control samples (P<0.001). Cutaneous HPVs predominated. One patient had HPV16 in samples taken four years apart without evidence of associated lesions or malignancy. Transplant recipients were more likely than controls to have current cutaneous warts (P<0.001), fewer sexual partners (P=0.001), and to have never consumed alcohol (P=0.01). Among the transplant group, the risk of an HPV-positive sample was higher among older patients (P=0.05), and those with past cutaneous warts (P=0.04). This study extends previous surveys by encompassing overt and asymptomatic infection, a broad spectrum of cutaneous and genital HPVs, and by providing new data on risk factors for oral HPV infection.