The natural history of squamous intraepithelial lesions (SILs) in the anal canal of HIV-infected men is incompletely understood. We assessed the incidence and factors associated with SIL and invasive anal squamous cell carcinoma (IASCC) among HIV-infected men with normal cytology at baseline. We performed a single-center prospective cohort study [men who have sex with men (MSM) and men who have sex with women (MSW)]. The incidence of anal canal SIL (low grade and high grade) and IASCC were estimated and predictive factors analyzed. The study population comprised 297 HIV-infected men with a normal cytology result and no anal human papillomavirus (HPV)-related diseases. Of these, 251 (85%) had at least one evaluable set of cytology data during follow-up (172 MSM, 79 MSW). The median follow-up time was 4 years. The cumulative incidence of SIL was 43% (107/251): 52% in MSM (90/172) and 22% in MSW (17/79),  < 0.0001. The incidence rate of SILs was 109 (95% confidence interval = 90-132) per 1000 person-years: 142 in MSM and 49 in MSW,  < 0.0001. HPV infection, receiving antiretroviral treatment (ART), and being MSM were independently associated risk factors. The incidence of IASCC was 0.15 per 1000 person-years among MSM and 0 in MSW. HIV-infected men, both MSM and MSW, are at high risk of developing SIL despite having a normal anal cytology at baseline. The incidence of anal canal SIL was higher among MSM, but was also remarkable among MSW. Independent risk factors associated with SIL were being HIV-infected MSM at high risk for acquisition of STIs, time on ART, and HPV infection.

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