Human papillomavirus (HPV)-related anal cancer incidence is rising in men who have sex with men (MSM). Effective screening strategies exist, but many patients are lost to follow-up (LTF). We studied factors impacting screening compliance to recommended annual screening visits. Retrospective chart review identified MSM with anal dysplasia. MSM were grouped as regular screeners (regular to follow-up RF) (≥1 visit/year), lost to follow-up (LTF) (>1 year since previous screening) and LTF who then returned for screening (lost came back LCB). From June 2007 to March 2008, subjects completed a questionnaire in-person at the time of screening or via telephone (LTF). Questionnaires were completed after anal dysplasia diagnosis. One hundred and ninety-five MSM were enrolled (96 RF, 50 LTF and 49 LCB). RF were compliant for 4.8 years; LTF were lost for 2.3 years. LCB were previously lost for 5.6 years before returning. Mean knowledge score of screening procedures was larger in RF versus LTF (P < 0.001). MSM with more sexual partners in the past six months were more likely to be LCB versus LTF (P = 0.05). RF were more likely to describe their HPV diagnosis as 'upsetting' (P = 0.003). RF were more likely driven by physical symptoms versus LTF (P = 0.002). MSM with high-grade intraepithelial lesions (HSIL) were more likely to be RF versus those with low-grade intraepithelial lesions (P = 0.001. Positive predictors for screening compliance include an upsetting experience during the HPV diagnosis, physical symptoms driving the initial visit and HSIL. Engaging patients in a firm, salient approach may facilitate follow-up compliance.