Objective. Little information exists regarding high-risk human papillomavirus (HPV) subtypes in human immunodeficiency virus (HIV) patients with atypical squamous cells of undetermined significance (ASCUS) cytologic results. This study aimed to characterize further HPV prevalence and high-grade cervical intraepithelial neoplasia (CIN) in this subpopulation of patients. Materials and Methods. This is a secondary analysis of a prospective HPV natural history study involving 200 HIV-seropositive patients. We analyzed 102 patients from this cohort with a cervical cytologic diagnosis of ASCUS for high-risk and low-risk HPV prevalence, clearance of HPV infection, progression or regression of cervical cytologic abnormality, and prevalence of CIN 2 or worse at the time of indicated colposcopy. Pap smears were slide-based and HPV testing was performed using nested polymerase chain reaction. Results. Overall prevalence of ASCUS in the HIV population was 20% (40 of 200 patients). Despite a high prevalence of all HPV subtypes (74 of 102 subtypes; 73%), high-risk subtypes were present in only 32% of patients (33 of 102 patients) with ASCUS cytologic results. In 5 of 42 patients (12%) undergoing colposcopy within 6 months of ASCUS cytologic results, CIN 2 or worse was found. Sensitivity, specificity, positive predictive value, and negative predictive value of a high-risk or intermediate-risk HPV test for CIN 2,3 were 100%, 70%, 31%, and 100%, respectively. Progression to high-grade intraepithelial lesion cytologic results after ASCUS was rare (5/64 evaluable patients; 8%) but persistence of low-grade cytologic results (ASCUS or low-grade intraepithelial lesion) was common (43/64 evaluable patients; 67%). Conclusions. Despite a high rate of HPV infection in the HIV population with ASCUS Pap results, high-risk HPV subtypes represent a minority of patients and are significantly associated with presence of high-grade CIN at colposcopy. High-risk HPV testing should be investigated further in the HIV population.