Two clinical forms of functional dyspepsia (FD) are listed in the Rome III criteria: postprandial distress syndrome (PDS) and epigastric pain syndrome (EPS), differing in the recurrence of ailments depending on the diet. Continuous EPS (CEPS) is observed in some EPS patients, also at night, but its cause is still unknown. We showed previously that melatonin (MEL) homeostasis may be associated with FD. In the present work we evaluated selected components of melatonin homeostasis in patients with CEPS. The study included 30 patients with CEPS, 21 women and nine men, aged 21-49 years and 30 control subjects (EPS excluded); organic and mental diseases, as well as Helicobacter pylori infection, were excluded in both groups. The average severity of abdominal pain in the last three months was estimated in a 10-point scale (Visual Analog Scale). The levels of mRNA expression of arylalkylamine-N-acetyltransferase (AANAT) and hydroxyindole-O-methyltransferase (HIOMT), the main components of MEL homeostasis, were determined in gastric mucosa with real time PCR. The fasting serum level of MEL (at 09: 00 a. m.) and circadian urine excretion of 6-sulfatoxymelatonin (6-HMS) were determined with ELISA. AANAT expression in antral mucosa of control subjects was 1.76 +/- 0.41, in the gastric body 1.35 +/- 0.38, and in the dyspeptic group 1.42 +/- 0.38 (p < 0.05) and 0.92 +/- 0.55 (p < 0.05), respectively. HIOMT expression in the control was 2.05 +/- 0.70 in the antrum and 1.57 +/- 0.69 in the body and in the CEPS group, it was: 1.51 +/- 0.57 (p < 0.05) and 0.74 +/- 0.31 (p < 0.001), respectively. MEL concentration (pg/mL) was 9.41 +/- 3.09 in the control group and 5.62 +/- 1.34 (p < 0.01) in the CEPS group. Urinary 6-HMS excretion (mu g/24 h) was 11.40 +/- 4.46 in the controls and 7.68 +/- 2.88 (p < 0.05) in the CEPS. Moreover, a negative correlation was found between the tested parameters and severity of epigastric pain. These results indicate that patients with CEPS may display low level of AANAT and HIOMT expression in gastric mucosa, resulting in decreased MEL synthesis.