Abstract Background Cardiac troponins(cTn) are in a key role in the diagnosis of acute myocardial infarction (MI). Minor cardiac troponin elevations are also common after strenuous exercise, while limited evidence suggests this elevation consists mostly of smaller cTn fragments. Purpose We aimed to determine if our novel cardiac troponin assay, measuring long molecular forms of cardiac troponin (long cTnT) can differentiate cardiac troponin elevation associated with strenuous exercise from that seen in MI. Methods In a Proof-of-Principle study, we developed a simple time-resolved immunofluorometric assay based on europium chelate labels for the measurement of long cardiac troponin T molecules, which showed high accuracy in discriminating between cTn elevations in MI and end-stage renal failure. In the present study, we compared the characteristics of cTn release after a marathon race and Type 1 MI using an improved version of the long troponin test and a commercially available cTnT test. Troponin composition was analyzed in heparin plasma samples taken from 45 runners <1h after marathon race and from 45 patients with Type 1 MI. The concentration of long cTnT was measured with a novel immunofluorometric assay, total cTnT was measured with a commercial high-sensitivity cTnT assay, and the ratio of long to total cTnT (troponin ratio) was determined. Results Conventional cTnT exceeded the upper reference limit in 37 (82%) runners with a median concentration of 25.0 (IQR 16-36)ng/l. Median long cTnT concentration was 4.1 (IQR 2.4-5.8)ng/l. The median total and long cTnT concentration and the troponin ratio were higher in patients with MI than in marathon runners (p<0.001). Troponin ratio decreased (r=-0.497, p<0.001) in marathon runners and increased (r=0.466, p=0.001) in patients with MI with increasing troponin release (Figure 1). In the receiver operating characteristics curve analyses of all patients with cTnT release >14ng/l, long cTnT showed good predictive power with area under curve 0.969 (CI95% 0.939-1.000) in discriminating marathon runners from MI patients. Conclusions Our novel highly sensitive long cTnT immunoassay shows that the troponin release after strenuous exercise is composed mainly of smaller troponin fragments. Our test could be useful in separating benign cTnT elevations caused by exercise from those of acute MI.