The performance of cytologic screening and its correlation with histology and polymerase chain reaction (PCR) detection of human papillomavirus (HPV) DNA have not been evaluated in populations with a low prevalence of anal intraepithelial neoplasia (AIN). The objective of the current study was to analyze the significance of abnormal smears relative to the histology and PCR detection of HPV DNA. A cytologic smear and a viral sample were taken in 300 consecutive patients undergoing surgery (Milligan-Morgan hemorrhoidectomy and/or fissurectomy) who gave their informed consent. The cytologic smear was normal in 216 of 290 patients (74.5%). Four high-grade and 19 low-grade intraepithelial neoplastic lesions were identified. In 5 patients, high-grade lesions could not be excluded, 30 lesions were of undetermined significance, and there were 16 cellular modifications with a non-neoplastic appearance. The PCR test for HPV was positive in 18.7% of patients, and a high-risk genotype was identified in 63.6% of positive samples. Histologic examination of the surgical samples was normal in 92.3% of patients. The 23 AIN samples were distributed as follows: 13 grade 1 AIN (AIN1), 6 AIN2, and 4 AIN3. The sensitivity of cytologic smears and PCR for detecting AIN was 56% and 60.8%, respectively, and specificity was 77% and 84.5%, respectively. Combining the 2 tests increased sensitivity to 78% but decreased specificity to 68%. Compared with a large surgical sample, anal cytologic Papanicolaou smears and HPV PCR exhibited sensitivity and specificity that varied, depending on the risk of HPV infection and AIN. Positive HPV DNA screening increased with AIN grade, and high-risk HPV testing was particularly helpful.