Human papillomavirus is a common sexually transmitted infection associated with cervical dysplasia. We investigated the extent of urethral human papillomavirus infection by performing urethrocystoscopy on 90 men who presented to a sexually transmitted disease clinic with external meatal warts. A total of 83 men underwent biopsies and in 49 human papillomavirus typing was done. Of 90 men with external meatal warts 75 (83.3%) had no other warts, while 15 (16.7%) also had more proximal lesions. Only 5 men (5.6%) had lesions at or beyond the pendulous urethra. Of the 90 men 12 (13.3%) had 2 warts, 3 (3.3%) had 3 warts and none had more than 3 warts. A total of 39 men had human papillomavirus type 6/11, 1 had type 31/33/35 and 9 were negative for human papillomavirus antigens. Histological evaluation of biopsies showed no dysplasia. Our study confirms that the frequency of internal urethral warts is low. Human papillomavirus infection was not associated with urethral dysplasia.