Background Although endomyocardial biopsy (EMB) plays a crucial role in the final diagnosis in patients with heart failure of unknown etiology, the invasive nature of this technique limits its clinical application in China. The purpose of this study was to evaluate the clinical application of EMB in diagnosing cardiomyopathy with unexplained etiologies in China. Methods Fifty-three consecutive patients (38 males, age 14-67 years, median 43 years) were included in the study who were initially diagnosed as unexplained cardiomyopathy and under EMB biopsy in Peking Union Medical College Hospital from 2006 to 2009. The patients were clinically divided into four groups: dilated, hypertrophic, restrictive and unclassified cardiomyopathy. Biopsies were performed via right intal jugular vein with the use of the bioptome under fluoroscopic guidance. Three to five endomyocardial samples were taken from each patient for light microscopy examination and one sample for electron microscopy was taken if necessary. For each patient, an initial clinical diagnosis, an EMB diagnosis and a final diagnosis prior to discharge were established. All the data were compared and analyzed for the evaluation of clinical utility of EMB in China.Results In 26 patients initially diagnosed with restrictive cardiomyopathy (RCM), the etiology of the condition was finally diagnosed using EMB in 15; including 13 amyloidosis and two eosinophilic myocarditis. We employed EMB in 19 patients clinically diagnosed as dilated cardiomyopathy and detected viral myocarditis in one patient, cardiac involvement due to polymyositis in four and doxorubicin-induced cardiomyopathy in one. In five patients with severe left ventricle hypertrophy undergoing EMB, one patient was diagnosed as autophagic vacuolar cardiomyopathy and one as mitochondrial disease. In the remaining three patients with unclassified cardiomyopathy, EMB revealed infiltration of eosinophils as the cause of atrial ventricular block in one patient. Final diagnoses were made in 24 of the total 53 patients (45%) based on the combination of EMB and clinical data. Transient atrial ventricular block in a patient with prior complete left bundle branch block was the only complication occurred during the procedures.Conclusion The clinical application of EMB is safe. The combination of EMB and clinical data produced a better understanding of the mechanisms behind the clinically diagnosed cardiomyopathy in China.