Abstract Aim To evaluate the pepsin and oxidative stress markers in exhaled breath condensate (EBC) in patients with gastroesophageal reflux disease (GERD). Patients and Method Patients with a presumptive diagnosis of GERD with recurrent respiratory and gastrointestinal problems aged between 2 and 14 years were included in the study. All patients underwent pH monitoring. Patients with a reflux index (RI) ≥ 4 were assessed as the reflux group, and those with an RO < 4 were assessed as the non-reflux group. Pepsin levels and oxidative stress markers NO metabolites (NOX) and total sulphydrile (TSH) levels were measured in the EBC. Results There were 24 patients in the reflux group RI 17.6 (6.6–46.4) median, interquartile range and 23 in the non-reflux group RI 0.8 (0.5–1.9) (p < 0.001). Pepsin levels in the EBC were below the level of detection. The median levels of NOx in the EBC of children with reflux 13.7 μmol/L (7.3–24.5) were lower in than non-reflux group 21.0 μmol/L (14.0–25.2) (p = 0.034). There was a negative correlation between reflux index and NOX levels in EBC (rs: − 0.331, p = 0.023). In contrast, there was no difference in TSH levels between the reflux and non-reflux groups 37.4 μmol/L (30.2–44.6) vs 40.1 μmol/L (37.4–44.9), respectively, (p > 0.05). Conclusion Decreased levels of NOX in patients with GER disease suggest increased oxidative stress in airways of these patients.