An automated and rapid method for quantifying malondialdehyde (MDA) in breath condensate was developed and validated. The method is based on derivatisation with thiobarbituric acid, HPLC separation and fluorescence detection and is optimised for determination of MDA in breath condensate. Sample collection is non-invasive and simple. The detection limit (4.1 nM) is low, precision is good and the analysis time is short. The response is linear in the concentration range of 0.020 to 1.0 microM. Samples could be stored for 1 month at -20 degrees C and for 3 months at -80 degrees C without losses. Using this method, there was no statistically significant difference between patients with asthma and patients without asthma. However, among females, subjects with asthma had higher MDA levels as compared to females without asthma (0.17 vs. 0.12 pmol/s, p=0.04). The use of the method when studying airway inflammation has to be further evaluated.