Development of malignancy is a pending threat for patients with inflammatory bowel disease (IBD). Aim of this study was to analyze cervical dysplasia and infection with human papilloma virus (HPV) in patients with IBD. This was a prospective, single center cohort study in Germany. Consecutive IBD patients admitted to the Department of Gastroenterology were sent to Gynecology, where a questionnaire was answered and gynecological examinations including a smear for cytology and HPV were taken. Participants of a general screening program constituted controls. Descriptive statistics, 95% confidence intervals and odds ratios were calculated. A total of 101 patients were recruited of which 99 patients participated. Analysis showed a significant (p = 0.05) difference between the prevalence of abnormal smears in patients with (22%) and without (6%) immunosuppressive therapy, while the latter had cervical abnormalities comparable with healthy controls (5%). All immunosuppressants showed similarly high risks for abnormal smear results. Only 11/99 (11%) patients had positive high-risk HPV tests, which is comparable with general population. The prevalence of abnormal cervical smears is higher in IBD patients compared to healthy individuals, but the difference is confined to patients with IBD and immunosuppressive therapy. Annual screening is advisable.