Recently, the results of many experimental investigations have shown that melatonin possesses gastroprotective properties. On the other hand its role in pathogenesis of upper digestive tract diseases in man still remains unclear. The aim of the study was to investigate nocturnal secretion of melatonin in patients with functional and organic diseases of the upper part of digestive tract. The investigations were carried out in 149 persons, aged 21-51 years, including healthy subjects (group I, n=30), and patients with non-erosive gastroduodenal reflux (NERD, group II, n=24), with gastroesophageal reflux disease (GERD, group III, n=25), with functional dyspepsia (FD, according to the Rome III Criteria, group IV, n=36) and with recurrent duodenal ulcer (DUD, group V, n=34). Diagnoses were established on the basis of endoscopic imaging and histological examination, 24-hour pH-metry and laboratory tests. Melatonin serum concentration was measured with ELISA method. Blood samples were taken for examination in red-lighted room at 10 p.m. and on the following day at 2 and 6 a.m. The highest concentration of melatonin in all examined groups was determined at 2 a.m. The average melatonin concentration in healthy subjects was 34,7 +/- 4,8 pg/ml. In patients with GERD and DUD melatonin concentration was lower than in healthy subjects - 27,2 +/- 8,5 pg/ml and 25,5 +/- 6,2 pg/ml respectively (p < 0,05; p < 0,01). The highest concentration of melatonin was found in patients with NERD and FD - 43,2 +/- 10,8 pg/ml and 42,4 +/- 10,1 pg/ml (p < 0,01; p < 0,05). The findings of this study support the notion that melatonin exerts beneficial influences on the upper digestive tract. It is likely that high or relatively correct secretion of melatonin is sufficient to prevent peptic changes in esophageal and duodenal mucosa.