In order to investigate the contribution of eicosanoids to human oesophageal functions and disorders (gastrooesophageal reflux, GOR and reflux oesophagitis, RO), we have used a selected ion monitoring gas chromatographic/mass spectrometric methodology to quantify the cyclooxygenase and lipoxygenase products biosynthesized in vitro by endoscopic mucosal biopsy specimens. Prostaglandins (PGs) were quantified as MEMOTMS derivatives and HETEs, as hydrogenated methyl ester of tert-butyldimethylsilyl) ether derivatives. PGE2, PGF2 alpha appeared as the major prostanoids, whereas 12HETE seemed to be the major lipoxygenase product. In the case of GOR or RO, biosynthesis of PGE2 was dramatically increased, while no change could be detected for 12HETE. PGE2 increase seems to be related to inflammatory reaction, in which its exact role remains unclear. Moreover, it cannot be excluded that PGE2 is a side product which might be protective to the oesophageal mucosa.