Background Environmental factors, including sleep disturbances, have been associated with the risk of flare in inflammatory bowel disease (IBD). Symptoms, treatment side effects and pro-inflammatory status have been shown to have an effect on sleep quality and duration. Previous studies showed that around 44% of IBD patients suffer from sleep disorders. We aimed at determining the prevalence of sleep disturbances in IBD patients, as compared with normal controls, and factors associated with disturbances. Methods We conducted a cross-sectional study on adult patients included in the Swiss IBD cohort study. We excluded pregnant women and night workers. We used the HypnoLaus cohort as a control population. Demographics, clinical, treatments, SF-36 and IBDQ (bowel, emotional, social and systemic sub-scores) quality of life data were extracted from the SIBDCS. We sent patients a questionnaire comprising the Pittsburgh Sleep Quality Index (PSQI), Epworth score (ESS), and Restless Leg Syndrome (RLS) Score. We assessed differences regarding those scores between IBD and controls. We performed logistic regression analyses to evaluate factors associated with sleep disturbances in the IBD population. Results A total of 1139 patients answered to the questionnaire: 613 CD, 526 UC, 47% males, mean (SD) age: 50(15) years, median (IQR) disease duration: 15 (15) years. One out of five patients had extraintestinal manifestations (EIM). Forty-one percent were receiving biologic treatment (UC: 27.6%, CD: 53.0%). We found 906 age-sex-BMI matched controls who answered the PSQI, ESS and RLS. A significantly higher proportion of IBD patients had impaired sleep quality (PSQI) as compared with the control population (61.3% vs. 33.9%; p < .001). The proportion of IBD patients with ESS sleep deficiency (incl. daytime sleepness) was significantly higher as compared with controls (32.5% vs. 23.4%; p < .001). We also found a higher prevalence of RLS in IBD than in controls (27.8% vs. 13.0%; p < .001). Factors associated with impaired sleep quality were female gender (OR=1.37; p = .048), IBDQ bowel (OR=1.03; p = .033) and IBDQ systemic (OR=0.83; p < .001). ESS sleep deficiency was associated with IBDQ emotional (OR=1.02, p = .050) and social (OR=0.95; p = .046). RLS was associated with increased age (OR=1.02, p < .001), being a smoker (OR=1.54; p = 0.035), prior steroid use (OR=2.17, p = .001) and IBDQ emotional (OR=0.95, p = .005). Conclusion Sleep disturbances are highly prevalent in IBD patients compared with the control population. In IBD, sleep disturbances were associated with IBD-specific quality of life, but not with disease activity and EIM. Future studies should address whether early detection and active management of sleep disorders might influence disease control and long-term outcomes.