Anal squamous intraepithelial lesions (ASIL) are common in homosexual and bisexual men, and high-grade ASIL (HSIL) in particular may represent an anal cancer precursor. Cervical cytology is a useful screening tool for detection of cervical HSIL to prevent cervical cancer. To assess anal cytology as a screening tool for anal disease, we compared anal cytology with anoscopy and histopathology of anal biopsies. A total of 2958 anal examinations were performed on 407 HIV-positive and 251 HIV-negative homosexual or bisexual men participating in a prospective study of ASIL. The examination consisted of a swab for anal cytology and anoscopy with 3% acetic acid and biopsy of visible lesions. Defining abnormal cytology as including atypical squamous cells of undetermined significance and ASIL, the sensitivity of anal cytology for detection of biopsy-proven ASIL was 69% (95% confidence interval: 60 to 78) in HIV-positive and 47% (95% confidence interval; 26 to 68) in HIV-negative men at their first visit and was 81% and 50%, respectively, for all subsequent visits combined. The absence of columnar cells did not affect the sensitivity, specificity, or predictive value of anal cytology. Anal cytology may be a useful screening tool to detect ASIL, particularly in HIV-positive men. The grade of disease on anal cytology did not always correspond to the histologic grade, and anal cytology should be used in conjunction with histopathologic confirmation.