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Prevalence of high-grade anal intraepithelial neoplasia, the human papillomavirus-associated putative anal cancer precursor, is high in HIV-infected men who have sex with men, but less is known about its prevalence in other HIV-infected subgroups. Similarly, the prevalence of abnormal cytology, used as a screen, is not well-defined in these subgroups.This study aimed to estimate the prevalence of abnormal cytology and anal intraepithelial neoplasia in a primary care HIV-infected population.This investigation was designed as a cross-sectional study.This study took place at a Ryan White–funded clinic.Included in the study were all (n = 779) HIV-infected patients receiving primary care services between March 2006 and March 2008.The main outcome measures were anal cytology and high-resolution anoscopy results.The prevalence of abnormal cytology was 43%: 62% in men who reported receptive anal intercourse, 39% in women who reported receptive anal intercourse, and 25% in all others (P trend <.0001). High-grade anal intraepithelial neoplasia prevalence was 27%: 44% in men who reported receptive anal intercourse, 26% in women who reported receptive anal intercourse, and 10% in all others (P trend <.0001). Two patients had squamous-cell cancer. Independent predictors of dysplasia were CD4 at screening, receptive anal intercourse, sexual orientation, and history of human papillomavirus disease. Anal cytology and histology findings were not well correlated.The study population may not be representative of the general HIV-infected population, there were differences between screened and unscreened patients and between patients with abnormal cytology who had high-resolution anoscopy and those who did not, only patients with abnormal cytology had high-resolution anoscopy, and there were possible misclassification errors and uncontrolled possible confounders.High-grade anal intraepithelial neoplasia is relatively common in HIV-infected patients regardless of sexual practice. Although risk increases with receptive anal intercourse, patient-provided information on this sexual practice should not be used as a determining factor for screening. Strategies to prevent anal cancer are necessary for all HIV-infected patients.