Persistent human papillomavirus infection in human immunodeficiency virus (HIV)-infected individuals has been strongly associated with anal squamous cell carcinoma. The incidence of anal squamous cell carcinoma continues to increase in this population despite advances in HIV therapy. There are few studies describing the prevalence of anal cancer precursors, treatment outcomes, and associated factors among HIV-infected populations in the southern United States. A retrospective chart review was performed on 355 HIV-infected patients from a Southern HIV clinic who were 18 years or older and had received at least one anal Pap smear. Demographic and clinical variables were collected. Descriptive statistics, single variable, and multivariate logistic regression analysis were performed to evaluate for predictors of high-grade squamous intraepithelial lesion (HSIL). Odds ratios and 95% confidence intervals were constructed for independent measures. After the first anal Pap smear, 38.3% (70/183) of patients with abnormal results were lost to follow-up. Comparing patients with biopsy proven HSIL versus low-grade squamous intraepithelial lesions, patients were less likely to have HSIL if they had a higher CD4 count (odds ratio, 0.81; 95% confidence interval, 0.72-0.93; P = 0.0022). Treatment success after the first round of treatment for topical and infrared coagulation therapy was 36.7% (18/49, all therapy types), and of those who achieved biopsy proven treatment success at follow-up screening, 94.4% (17/18) required subsequent therapy. Patients with a higher CD4 count were less likely to have HSIL. CD4 nadir, number of sexual partners, and race/ethnicity were not significantly associated with the presence of HSIL.