Human papillomavirus (HPV) infection strongly correlates with the development of anal intraepithelial neoplasias and carcinomas; however, few studies have characterized the distribution of the specific subtypes of the virus in the varying grades of dysplasia. This report characterizes the distribution of HPV 16/18 in surgical specimens with anal intraepithelial neoplasia (AIN) I-III and histological variants of anal carcinoma. A total of 111 anal surgical specimens with no dysplasia (10), AIN I-III (53), and anal carcinomas (48) were evaluated for the presence of high-risk HPV infection and subtyped by nested PCR or the Invader Assay. High-risk virus types were detected in progressively greater number of anal intraepithelial lesions from 56% in low grade to 88% in high grade. Type 16 was the prevalent subtype and was noted in 28% of low grade and 68% of high-grade lesions. Moderate dysplasias showed type 16 in 20%, a prevalence similar to that in low-grade lesions. The non-16/18 subtypes of the virus predominated and were present in 50% of the cases. Most (89%) squamous carcinomas were associated with high-risk viruses, 68% with type 16, a prevalence similar to that noted in high-grade dysplasia. Non-16/18 subtypes were encountered more frequently in squamous carcinomas from immunodeficient individuals (57% cases) as compared with immunocompetent individuals (18% cases). The similarity in the prevalence of type 16 in high-grade dysplasia and squamous carcinomas suggests that anal intraepithelial lesion III is the true precursor of squamous carcinoma and warrants aggressive management. Anal intraepithelial lesions II showed a virus distribution that was similar to low-grade dysplasia. In addition, a subset of these that were associated with type 16 or 18 showed progression, whereas those associated with non-16/18 subtypes regressed, thereby raising the possibility of conservative management for these lesions.