Background: Anal cancer is rare in the general population in both genders in the US, but an increased incidence of anal cáncer (AC) has been reported among people living with HIV-1 infection (PLWH) and little is known among the population in South US. Methods: In a retrospective study design, electronic health records from 2006 to 2018 were reviewed in a HIV clinical cohort at the University of Alabama at Birmingham. Associations of demographic, sociodemographic, and HIV-clinical indicators were examined in univariate analyses between high-grade squamous intraepithelial lesions (HSIL) and AC cases and condition-free individuals. Factors for anal/rectal cytology screening tests among PLWH were also assessed over time. Ages at onset of anal cancer were compared with the general US population reported by the National Surveillance, Epidemiology, and End Results Program. Results: A total of 79 anal HSIL (96% men) and 43 cancer (100% men) patients were observed along with 4367 HSIL/cancer-free patients (75.9% men). HSIL (P < 0.0001) and AC (0.0001 < P < 0.01) were associated with being men who have sex with men (MSM). An incidence of 258 per 100,000 person-year was observed among this clinical cohort of PLWH. PLWH who were 45–54 years appeared to be at highest risk of AC (58.1%), as compared to those 55–64 years in the general population. Overall, 79% of PLWH anal cancers were diagnosed among those under 55 years (vs 39.5% in general population) indicating early onset of AC. In total 29.1% of HSIL and 44.2% of AC patients had not received an anal/rectal cytology examination 1 year prior to diagnosis. Conclusion: AC incidence among HIV-infected men was 161 times higher than general population with an earlier age of onset/diagnosis. Many patients with AC had missed screening opportunities that could potentially have captured neoplasia in pre-cancerous stages. AC-related screening guidelines need to be integrated into routine clinical care, especially among PLWH at highest risk such as MSM and those with lower CD4 counts.