Basal level multiple deletions in the heart mitochondrial (mt) DNA of patients with dilated cardiomyopathy were analyzed with the recently developed long PCR technique. The amplification of the whole mitochondrial genome and the length dependent preferential amplification ensure that all existing deletions are detected simultaneously. Primer shift long PCR proved the specificity of our method in the detection of deletions. We used primers that were 15644 bp and 13765 bp apart, which comprised almost the entire mitochondrial genome, detected a total of 14 kinds of deletions in 18 out of the 40 endomyocardial biopsy samples from patients with dilated cardiomyopathy. These deletions ranged in size from 3.3 kb to 12.6 kb. The proportion of the deleted to wild-type mtDNA was calculated to be less than 9% for any of these deletions. Aged patients had a comparatively higher proportion. Deletions were rarely found in mtDNA of leukocytes from the same group of patients and of 38 additional patients, as well as in myocardia of 25 normal controls (P < 0.01). No deletion was found in leukocytic mtDNA of the 21 control subjects. It is therefore concluded that cardiomyopathic heart has a high frequency of mtDNA deletions. With regard to the low quantity and the cumulative nature of these deletions by aging, they could have only little pathogenic effect on the development of dilated cardiomyopathy, but rather be a sign of increasing stress of the heart promoting the damage of mtDNA.