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To investigate whether coronary artery disease (CAD) burden is associated with plasma levels of the myocardial biomarkers Troponin I (TropI) and NT-proBNP in a large population-based sample using a cross-sectional design. Coronary computerized tomography (CT) angiography was performed in 25,859 subjects without a history of atherosclerotic disease from SCAPIS study (age 50–65, 52% women). TropI and NT-proBNP were measured in plasma. Segment involvement score (SIS) was the primary exposure and TropI the primary outcome. Both SIS and coronary artery calcium score, were associated with TropI levels following adjustment for age, sex and multiple confounders (p < 0.001), with similar relationships in men and women. Proximal segments from all three coronary arteries were related to TropI levels independently of one another. Adding TropI to traditional risk factors marginally increased discrimination of atherosclerosis as compared to risk factors alone (C-statistics + 0.0005, p = 0.014). SIS was related also to NT-proBNP levels, mainly in men, but with lower estimates than TropI. The burden of CAD was related to TropI levels in both men and women. All three major coronary arteries contributed to this relationship. Adding TropI to traditional risk factors resulted in only marginally improved discrimination of coronary atherosclerosis.