The objective of the study was to investigate magnetocardiography (MCG) capabilities in diagnosis of ischemic and inflammatory myocardial injuries using new MCG markers of the spatio-temporal organization of myocardium excitation. We investigated 34 healthy volunteers, 62 patients with ischemic heart disease (IHD) and 32 patients with acute myocarditis. MCG-mapping of patients was performed at rest on the 7-channel MCGscanners «Cardiomagscan» V 3.1 (Company KMG, Ukraine) in non-shielded MCG laboratory. Significant differences of MCG markers were revealed in the study groups. Patients with IHD and myocarditis differed from the healthy subjects by 8 of 11 markers. Analysis of the obtained data showed good capabilities of MCG in differential diagnosis. Application of discriminatory analysis allowed to get classification functions, which might be used (with 82 % accuracy) to qualify patients to the investigated categories. Thus, MCG was able to distinguish between healthy subjects and myocarditis patients and patients with IHD with sufficient sensitivity and specificity.