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Inflammatory bowel diseases (IBD) are chronic relapsing disorders that have a negative impact on quality of life. They can be highly disabling and have been associated with sleep disturbance. The aim of our study was to evaluate the sleep quality of a large cohort of IBD patients to identify possible associated cofactors. We prospectively recruited consecutive patients attending the IBD Unit of “Azienda Ospedaliera” of Padua from November 2018 to May 2019 and collected demographics and clinical characteristics. The patients completed the Pittsburgh Sleep Quality Index (PSQI), the IBD questionnaire (IBDQ), the IBD-Disability Index (IBD-DI) questionnaire, and the Hospital Anxiety and Depression Scale (9-HADS). A multivariate regression model was applied to assess independent risk factors of sleep disturbance among IBD-related variables, disability, quality of life, anxiety, and depression. We investigated the sleep quality of 166 patients with IBD, finding 67.5% of them suffering from sleep disturbance. In particular, low quality of life, presence of disability and extraintestinal manifestations were identified as independent risk factors of sleep disturbance. We discovered that all depressed patients were also affected by sleep disturbance, while we found no difference in sleep disturbance between patients with or without anxiety state. However, a positive correlation was reported between both anxiety and depression scores and PSQI score (Spearman correlation: r = 0.31 and r = 0.38 respectively). Our study showed that sleep quality is not directly associated with an active or inactive IBD state or with the ongoing treatment, but it is mostly correlated with the patients’ mood state, disability, and quality of life. Gastroenterologists and psychologists should join forces during clinical outpatients’ visits to evaluate emotional states for a better IBD management.