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Objective: This study aimed to determine the prevalence of anal intraepithelial lesions in women with histologic diagnosis of intraepithelial lesions of the lower genital tract., Materials and Methods: This was a cross-sectional study conducted at the Lower Genital Tract and Colposcopy Unit of Hospital de Clínicas "José de San Martín," University of Buenos Aires, Argentina. A total of 481 women with histologically confirmed low-grade and high-grade cervical, vaginal, or vulvar intraepithelial lesions were evaluated between 2005 and 2011. They were referred for cytologic samples and examination with high-resolution anoscopy. We obtained biopsy specimens of any suspicious colposcopic images., Results: Of a total of 481 patients, 404 (84%) were immunocompetent, 31 (6.4%) were HIV+, and 46 (9.6%) had other causes of immunosuppression. Moreover, of the 481 patients, 134 (27.86%) had anal intraepithelial neoplasia (AIN); 28 (5.82%) had high-grade AIN and 106 (22%) had low-grade AIN. Women with high-grade cervical intraepithelial neoplasia (CIN 2, 3) had 2 times the odds of developing AIN compared with women with low-grade CIN (CIN 1) (odds ratio = 1.91, 95% confidence interval = 1.1-3.6). Regarding localization, we found statistically significant difference between the frequency of vulvar and anal lesions. Women with vulvar condylomata and vulvar intraepithelial neoplasia (VIN) may be more likely to develop AIN., Conclusions: Immunocompetent women with CIN, vaginal intraepithelial neoplasia, or VIN may also present high-grade or low-grade anal intraepithelial lesions so we should consider AIN as part of multicentric disease of the lower genital tract. Cervical intraepithelial neoplasia, VIN, condyloma accuminatta, and vaginal intraepithelial neoplasia could be warning signs of anal intraepithelial lesions.