Squamous cell carcinoma of the anus is rare, but more common in men with human immunodeficiency virus (HIV). We describe our findings in 50 biopsies done on 37 HIV-positive men over 5 years. The men were referred from our HIV clinic for abnormal cytology on anal pap or anal condyloma. Thirty-seven patients were referred from the HIV clinic for abnormal cytology on anal pap or the presence of anal condyloma. Biopsies were done in the operating room using acetic acid to visually localize areas of dysplasia. If no abnormalities were seen, biopsies were taken from each quadrant of the anus. A retrospective review was done for biopsy indication, pathology, recurrence, and correlation with anal pap results. On initial biopsy, anal condyloma conferred the presence of anal intraepithelial neoplasia (AIN) in 64.7 per cent (11 of 17), abnormal paps in 83.3 per cent (10 of 12), and both in 50 per cent (3 of 6). Patients with anal condyloma had AIN in an average of 2.5 quadrants whereas those with abnormal cytology had AIN in 2.3 quadrants. Thirty-four of 50 biopsies showed abnormalities (68%), with AIN present in 32 cases, one case of carcinoma in situ, and one case of invasive carcinoma. Aldara was used nine times with improvement in four cases. In HIV-positive men, the presence of condyloma warrants surgical biopsy. Performing anal cytology on patients with anal condyloma did not increase the rate of positive results. Patients with AIN often had disease in more than two quadrants, making surgical excision problematic.