This study was initiated to assess the validity of eicosanoid determination in exhaled breath condensate by immunoassays. The results were compared to those obtained from liquid chromatographic methods with mass spectrometric detection and with the theoretical spiked amount of condensate. Therefore, spiked exhaled breath condensate was prepared achieving samples for comparison of identical aliquots. The three most often analysed inflammatory markers in the literature, i.e. leukotriene B-4, prostaglandin E-2, and 8-isoprostane-prostaglandin F-2 alpha were selected for comparison. Three concentrations of spiked and non-spiked breath condensate matrix were examined. There was an up to 800% overestimation of the eicosanoid quantities revealed by the immunoassay kits used in this study compared to the liquid chromatographic method with mass spectrometric detection which was in line with the nominal amount spiked. Full validation of immunoassay for the determination of inflammatory markers should be performed before further interpretations and consequences will be taken from the absolute values quantified by enzyme-immunoassays. For improving the accuracy of enzyme linked immunoassay (ELISA) results a collaborative work applying ELISA and LC-MS-MS should be performed in order to spotlight the advantages of the ELISA-method.