Hydrogen peroxide (H2O2) and nitrite (NO2-) in exhaled breath condensate have recently been suggested as non-invasive markers of airway inflammation. The goal of this study was to clarify the role of factors that may potentially influence the measurement of H2O2 and nitrite and to look for possible correlations among these inflammatory markers. H2O2 and nitrite values were assessed fluorometrically in breath condensate of 102 healthy children (age 4-18 years) and a detailed status of atopy (including history, lung function and skin prick test) was taken in all children. To find out the role of atmospheric nitric oxide, eNO and envNO were measured via chemiluminescence in association with the sampling of the breath condensate. Median (interquartile range) H2O2 was 0.51 (0.26 - 0.74) microM and nitrite was 3.3 (2.7 4.1) microM. A significant negative correlation between H2O2 and envNO was observed (r = -0.50; p < 0.0001). ENO was independent of envNO at our envNO range up to 56 ppb. No further correlation was found. The inflammatory markers in exhaled breath condensate H2O2, nitrite and eNO are not interrelated to each other in healthy children. Whereas eNO was not dependent on envNO values, high envNO values must be taken into account when measuring H2O2 in exhaled breath condensate.