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The diagnostic performance of cardiac magnetic resonance (CMR) has not been compared with that of other imaging modalities. Therefore, this study investigated the diagnostic capabilities of CMR and endomyocardial biopsy (EMB) in patients with heart failure (HF).We studied 136 patients with cardiomyopathy who underwent both CMR and EMB. Independent diagnoses were made according to the results of (i) CMR alone; (ii) EMB alone; (iii) clinical data plus echocardiogram; (iv) clinical data, echocardiogram, plus CMR; and (v) clinical data, echocardiogram, plus EMB. These diagnoses were then compared with the final diagnosis (gold standard) that was made using the complete clinical data, including EMB and CMR. The sensitivities of the diagnosis strategies of (i–v) relative to the final diagnosis were 67, 79, 86, 97, and 100%, respectively. CMR alone demonstrated better sensitivity for cardiac sarcoidosis and greater specificity for dilated cardiomyopathy than EMB alone. CMR also tended to show better sensitivity for hypertensive heart disease. There was no difference between the diagnostic capability of CMR and EMB for hypertrophic cardiomyopathy (HCM). However, CMR showed excellent sensitivity (100%) for apical and obstructive HCM, whereas EMB displayed better sensitivity for dilated HCM. Moreover, combined diagnosis with clinical data, echocardiogram, plus CMR achieved superior agreement with the final diagnosis in comparison with EMB alone.Non-invasive CMR demonstrated excellent diagnostic capability for patients with HF and was as effective as or superior to EMB. In particular, the use of CMR in combination with clinical data unrelated to EMB may provide excellent diagnostic accuracy for HF.