Keratosis reduces sensitivity of anal cytology in detecting anal intraepithelial neoplasia. 
To identify factors that may contribute to poor sensitivity of anal cytology in contrast to the sensitivity of anoscopy in heterosexual women.  We analyzed 324 patients with biopsy confirmed diagnosis of genital intraepithelial neoplasia (either vulva, vaginal, or cervical) from 2006 to 2011 who underwent both anal cytology and anoscopy.  Cytology, anoscopy, and biopsy results were recorded.  Biopsy specimens underwent independent analysis for quality of specimen.  Also, biopsy specimens were analyzed for characteristics that may contribute to correlation, or lack thereof, between anal cytology and anoscopic directed biopsy.  133 (41%) patients had abnormal anoscopy and underwent directed biopsy.  120 patients with normal anal cytology had anoscopy directed biopsies, resulting in 58 cases of AIN (sensitivity 9.4%; 0.039-0.199).  This cohort was noted to have extensive keratosis covering the entire dysplastic anal lesion.  18 patients yielded abnormal anal cytology.  Of these patients, 13 had anoscopic directed biopsies revealing 6 with AIN and absent keratosis (specificity 88.6%; 0.78-0.95).  The κ statistic for anal cytology and anoscopy was -0.0213 (95% CI=-0.128-0.086).  Keratosis reduces the sensitivity of anal cytology.  Furthermore, anal cytology poorly correlates with anoscopy in the detection of AIN (κ statistic=-0.0213).