The classification of anal intraepithelial neoplasia (AIN) in mucosal biopsies is subject to considerable interobserver variability. Previous studies have shown that Ki-67 and p16/CDKN2A immunostains aid detection of dysplasia in biopsy samples from the uterine cervix. The aim of this study was to determine whether Ki-67 and p16/CDKN2A immunolabeling enhanced diagnostic accuracy in the assessment of anal mucosal biopsies from patients with suspected human papillomavirus (HPV) infection. The study consisted of 75 cases that were originally interpreted to represent normal anal transitional zone (n=15), fibroepithelial polyp (n=10), condyloma accuminatum (n=10), low-grade AIN (AIN1, n=20), and high-grade AIN (n=20), including 10 cases each of AIN2 and AIN3. The histologic features of all cases were re-reviewed and categorized based upon consensus agreement, which resulted in reclassification of 16 cases. Thus, the final study group consisted of 17 samples of normal anal transition zone, 14 fibroepithelial polyps, 6 condylomata accuminata, and 38 cases of AIN (11 AIN1, 16 AIN2, and 11 AIN3). Each case was tested for the presence of HPV DNA by a SPF10 polymerase chain reaction and LiPA25 genotyping assay and immunostained for Ki-67 and p16/CDKN2A. A positive Ki-67 result was defined as the presence of a cluster of at least 2 strongly stained epithelial nuclei in the upper two-thirds of the epithelial thickness. A positive result for p16/CDKN2A was defined as diffuse moderate-to-strong cytoplasmic and nuclear staining. None of the anal transition zone samples or fibroepithelial polyps showed Ki-67 or p16/CDKN2A staining. All condylomata and samples of AIN contained HPV DNA and showed positive Ki-67 labeling. All cases of high-grade AIN showed positive p16/CDKN2A staining. We conclude that Ki-67 labeling detects anal HPV-related changes with a high degree of sensitivity and specificity, whereas increased p16/CDKN2A staining is strongly associated with high-grade squamous neoplasia. These results indicate that a combination of these markers may aid interpretation of anal mucosal biopsy samples.