Background Inflammatory bowel disease (IBD), classified as Crohn’s disease or ulcerative colitis, is a chronic inflammatory condition that affects the gastrointestinal tract. Fatigue is a common symptom of IBD, even in periods of inactive disease; however, the cause of this fatigue is unknown. Studies have suggested that altered sleep patterns may be associated with the fatigue experienced by IBD patients. The aim of our study was to assess the sleep quality of patients with inactive IBD who report fatigue. Methods We conducted a prospective observational pilot study that examined IBD outpatients with inactive disease who had complaints of fatigue. Upon enrolment, patients underwent Level 1 diagnostic polysomnography for one night to measure objective sleep parameters. Patients were also asked to complete 3 validated questionnaires to assess fatigue, depression levels, and subjective sleep quality. Results Fifteen patients (7 with CD, 8 with UC) were enrolled in the study; their mean age was 38.6±11.6 years. IBD patients had a mean spontaneous arousal index of 20.0±9.7 arousals /h. Patients spent an average of 6.6%, 60.4%, 15.2%, and 17.9% of their total sleep time in stages N1, N2, N3 and rapid-eye-movement sleep, respectively. Four (26.7%) patients had obstructive sleep apnea, and 7 (46.7%) patients experienced periodic limb movements of sleep. Conclusions Patients with IBD experienced altered sleep patterns and high rates of sleep fragmentation. Further research is needed to determine how poor sleep quality can be treated in patients with IBD.