We report a case of verrucous carcinoma of the penis. A 62-year-old man, who presented with penile swelling and pain, was referred to our hospital. Although, penile tumor biopsy revealed no evidence of malignancy, the patient presented with penile swelling and discharge. The penis was surgically resected and urinary diversion was performed. The pathological examination of the resected glans revealed verrucous carcinoma of penis. Furthermore, in situ hybridization revealed human papilloma virus (HPV) infection. This clearly showed that the verrucous carcinoma of the penis resulted from the HPV infection. The patient has survived for 14 months after surgery without local recurrence or metastasis.