To investigate the optimal cytologic method for detecting anal intraepithelial neoplasia, the quality and diagnostic findings in 117 conventionally prepared smears and 191 CYTYC Thin-Preps were compared. Samples were obtained with a dacron swab from subjects participating in a longitudinal study of gay or bisexual men known as the Study to Help the AIDS Research Effort (SHARE). The smear takers were general clinicians who had no experience in obtaining cytologic specimens from the anus. Smears were entirely satisfactory in 48 (41.0%) subjects, limited for interpretation in 41 (35.0%), and unsatisfactory in 28 (23.9%). CYTYC preparations were satisfactory in 158 (82.7%) cases and unsatisfactory in 33 (17.3%). Insufficient cellularity was the most frequent reason for both unsatisfactory smears and CYTYC preparations, but air drying artifact was present in nearly every smear. Squamous intraepithelial lesions (SILs) were detected in four (4.5%) smears compared to 53 (33.6%) CYTYC slides. The detection of SIL correlated with the presence of glandular and metaplastic cells in CYTYC preparations, but this association disappeared if only satisfactory specimens were considered. In conclusion, CYTYC Thin-Preps were satisfactory twice as often as conventional smears (P < 0.005) and detected nearly eight times as many SILs (P < 0.005).