Melatonin in human beings is secreted from pineal gland and it is concerned with a wide range of functions. It plays an essential role in the physiology of the gastrointestinal tract, also it has an antiulcer effect, Disruption of melatonin might play a role in the pathogenesis of duodenal ulcer. In this study, melatonin level in urine was estimated in patients with duodenal ulcer at exacerbation and remission stages after exclusion of any other diseases in respect to normal control. Results revealed that there was a strong disturbance in melatonin rhythm was observed in duodenal ulcer patients and it was related to disease severity. So, urinary melatonin is a useful non-invasive diagnostic test for duodenal ulcer that may reflect disease activity.