This is the first report that mitochondrial (mt) DNA 'minicircles,' lacking replication origins, exist in the heart mtDNA of a young normal subject. A total detection system using 180 kinds of PCR primer pairs was recently devised to detect all possible deletions in mtDNA. To assess the reliability of the system, template mtDNAs were prepared from the heart muscle by three different methods including DNAase digestion. The methods for mtDNA preparation and the nuclear DNA contaminants were demonstrated to have few influences on the analysis. With not less than 95% accuracy, 52 types of deletions including 36 types of minicircles were detected in the subject's mtDNA. These results will give an insight to the mechanism of mtDNA deletion and to the relevance of the deletion with normal aging.