Thrombomodulin is a transmembranous glycoprotein of endothelial cells. In vitro it is a marker of endothelial cell injury. In vivo the levels of soluble serum thrombomodulin are regarded as parameters of disease activity in vasculitides and vasculopathies. However, the mean thrombomodulin values of different studies show marked concentration differences of the control values. The purpose of this study was to further investigate these differences. We examined 60 sera of patients with systemic lupus erythematosus (SLE) and 10 of healthy controls with three commercially available thrombomodulin ELISA kits for determination of their thrombomodulin concentration and correlation to disease activity. The disease activity of the SLE patients was determined with the SLAM-score. Raised thrombomodulin values were found in 58% (test A), 55% (test B) and 61.6% (test C). The thrombomodulin values significantly correlated with the SLE disease activity independently of the ELISA kit used (correlation coefficients: r=0.84 (test A), r=0.80 (test B), and r=0.65 (test C)). In addition, the correlation coefficients between the respective thrombomodulin values of the three tests were r=0.86 (test A to B), r=0.73 (test A to C) and r=0.79 (test B to C). However, significant differences between the results of the three ELISA kits were found between the detected thrombomodulin concentrations. The mean thrombomodulin concentrations of the controls were 25.6 ng/ml (test A), 3.53 ng/ml (test B), and 2.52 ng/ml (test C). Our results reveal that the soluble thrombomodulin values of all three commercially available ELISA kits significantly correlate with the disease activity of SLE patients. However, the results show significant differences in the determined thrombomodulin concentrations. A calibration would be required of the different ELISA kits in order to permit a direct comparison of the results of these thrombomodulin ELISAs. A general reference standard would be desirable for this calibration of all thrombomodulin ELISAs. However, this general reference standard has to be adapted to the distinct test conditions of all test kits as well as including all epitopes of thrombomodulin which are recognised by the different antibodies used in the respective test kits. At present, only ELISA kits from the same manufacturer should be used during a single study including any follow-up investigations.