The prognostic and diagnostic values of N-terminal pro-brain natriuretic peptide (NT-pro-BNP) in ischemic heart disease have already been investigated in many previous studies. Although NT-pro-BNP is affected by many factors, these previous studies did not strictly exclude them. This study included 110 patients who received coronary arteriography between November 2007 and September 2009. Excluded from the study were those patients who had clinical symptoms of heart failure, asynergy by echocardiography or left ventriculography (LVG), atrial fibrillation, prior myocardial infarction, valvular disease, lung disease, anemia or renal dysfunction. We compared the laboratory data, LVG and early transmitral-to-early diastolic annular velocity ratio (E/E _a) in echocardiography between the group with coronary stenosis and the group without it. NT-pro-BNP and the low-density lipoprotein/high-density lipoprotein ratio (LDL/HDL) independently associated with the presence of coronary artery stenosis (odds ratio of NT-pro-BNP, each 50 pg/ml 2.367, 95% confidence interval 1.302–4.303, p = 0.005). The area under the curve of the receiver-operating characteristic (ROC) curve of NT-pro-BNP, used to predict coronary artery stenosis, was 0.801 (0.719–0.883, p < 0.001). According to the ROC curve, the optimal cut-off level for predicting coronary stenosis was 64.3 pg/ml (sensitivity 82.5%, false-positive 34%). NT-pro-BNP is an attractive supplemental marker to predict the presence of coronary artery stenosis in a population that strictly excluded any affecting factors. In the population without factors affecting NT-pro-BNP, a slight increase suggests the presence of ischemic heart disease. The normal criteria for NT-pro-BNP in the patients undergoing coronary angiography may be much lower than the one currently used.