Abstract Background/aims Functional dyspepsia (FD) is often comorbid with sleep disturbance. However, it is not fully understood how sleep disturbance affects the pathophysiology of FD. We aimed to investigate the relationship between FD and sleep disturbance. Methods We prospectively enrolled 20 FD patients with sleep disturbance between December 2018 and July 2019. Patients took sleep aids for 4 weeks and filled out questionnaires before and after taking sleep aids. Pittsburgh Sleep Quality Index (PSQI), Epworth Sleepiness Scale (ESS), and Athens Insomnia Scale (AIS) were used to evaluate the severity of their sleep disturbance. Modified Frequency Scale for the Symptoms of Gastroesophageal Reflux Disease (mFSSG), Gastrointestinal Symptom Rating Scale (GSRS), and the Japanese version of Patient Assessment of Constipation Quality of Life (JPAC-QOL) were used to evaluate the severity of GI symptoms. Short-Form 36-Item Health Survey (SF-36) was used to evaluate QOL. Pre- and post-sleep medication values of questionnaires were compared. Results Among 20 enrolled patients, 16 completed the study protocol. Zolpidem, eszopiclone, and suvorexant were administered to six, nine, and one patient, respectively. Each median total score of questionnaires (pre-/post-sleep medication, respectively) was as follows: PSQI, 10.0/8.5; ESS, 12.5/5.0; AIS, 10.0/4.0; mFSSG, 21.0/16.0; GSRS, 44.0/31.0 (Pain in GSRS, 11.0/5.0); JPAC-QOL, 26.0/15.5; SF-36, 63.9/71.9. All of these results showed statistically significant differences between pre- and post-sleep medication (p
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