Background: Early diagnosis of ischemia is complicated by the poor sensitivity of standard tests and contraindication for stress testing in unstable angina patients. Magnetocardiography (MCG) imaging can be used for the rapid, non-invasive detection of ischemia at rest. Methods: We studied 125 patients with presumed ischemic chest pain. All were chest pain free at the time of scanning. A 6-minute resting MCG scan (CardioMag Imaging, Inc., New York, 9-channel system) was performed. Following the MCG scan, automated software data analysis was performed, and quantitative scores were automatically calculated for each subject. The presence of ischemia was determined after testing with serial troponins, stress testing, and/or coronary angiography. Results: The mean age was 59.4 ± 13.6 years. Most patients (86.4%) had non-ischemic 12-lead ECG and normal troponin (86.2%). Fifty-five patients (44.0%) were determined to be ischemic. The MCG sensitivity, specificity, positive and negative predictive value was 76.4, 74.3, 70.0 and 80.0%, respectively, for the detection of ischemia (p < 0.0001). Conclusions: MCG is a new rapid, non-invasive imaging tool able to detect repolarization abnormalities at rest consistent with ischemia in patients presenting with chest pain syndrome and normal or non-specific 12-lead ECG and normal troponin.