There are several methods for quantifying malondialdehyde (MDA), an oxidative stress biomarker, in exhaled breath condensate (EBC). However, due to the very diluted nature of this biological matrix, a high variability is observed at low concentrations. We aimed to optimize a 2,4-dinitrophenylhydrazine-based method using liquid chromatography coupled to tandem mass spectrometry and characterize the uncertainty associated with this method. We investigated the following parameters for the method validation: calibration linearity, limit of detection (LOD), precision, recovery, and matrix effect. The results were used to identify the main sources of uncertainty and calculating the combined uncertainty. The applicability of this method was evaluated in an ongoing epidemiological study by analyzing 164 EBC samples collected from different professional groups in subway environments. The optimized method was sensitive (LOD: 70 pg/mL), precise (inter-day variation < 19%) and accurate (recovery range: 92-106.5%). The calculated analytical uncertainty was the highest at the LOQ level and reached 23%. Although the analytical uncertainty was high at low MDA concentrations, it was significantly lower than that the observed inter-individual variability. Hence, this method performs sufficiently well and can be recommended for future use in epidemiological researches relying on between-subject differences.