In this work, capillary electrophoresis with contactless conductometric detection (CCD) was used for the analysis of the ionic content of exhaled breath condensate (EBC) to differentiate between healthy individuals and patients with gastroesophageal reflux disease (GERD). The exhaled breath condensate was collected using a miniature sample collection device and the content analyzed using a separation electrolyte composed of 20 mM 2-(N-morpholino)ethanesulfonic acid, 20 mM L-histidine, 2 mM 18-Crown-6 and 30 mu M cetyltrimethylammonium bromide. The separation of anions took less than 2.5 minutes, while the cations were separated in less than 1.5 minutes. The most significantly elevated ions in the group of patients suffering from gastroesophageal reflux disease were chloride, nitrate, propionate and butyrate. Although the number of subjects was too small to draw definite conclusions with regard to the discriminatory power of these ions, the pilot data are promising for EBC as a useful non-invasive alternative for other methods used in the diagnosis of gastroesophageal reflux disease.