In Europe, clinicians use so called high-sensitivity assays for the measurement of cardiac troponin I and T (i.e., hs-cTnI and hs-cTnT assays, also termed 5th generation assays) since several years. We aimed at performing a head-to-head comparison of two 5th generation assays in “real life use”.We studied 3588 consecutive patients presenting to an emergency department. We used both, a hs-cTnI assay from Abbott and a hs-cTnT assay from Roche in clinical routine. We assessed (1) the capabilities of hs-cTnI and hs-cTnT for the prediction of 3.7 year all-cause mortality; (2) discordant diagnoses of myocardial injury by hs-cTnI and hs-cTnT according to the European gender-neutral 99th percentile upper reference limits (i.e., 26 ng/L and 14 ng/L, respectively); and (3) analyte kinetics in patient with serial troponin measurements.With respect to prognosis of all-cause mortality, the AUC of hs-cTnI was 0.81 (95% CI, 0.80–0.82), and the AUC of hs-cTnT was 0.85 (95% CI, 0.84–0.86). With respect to discordant diagnoses, 21% of the 3588 patients were classified as having myocardial injury by hs-cTnT but not by hs-cTnI, and < 1% were classified as having myocardial injury by hs-cTnI but not by hs-cTnT. In the patients with serial blood sampling, the median delta values were 6.3 ng/L and 25% for hs-cTnI, and 4.2 ng/L and 16% for hs-cTnT.We found different characteristics of the Abbott hs-cTnI and the Roche hs-cTnT assays, especially when using the European gender-neutral 99th percentile upper reference limits. Clinically, these different characteristics are related to discordant results in the diagnosis and prognosis of patients presenting to an emergency department.