We examined the correlation of functional and structural abnormalities of cardiac mitochondria. created by pathogenic mutant mtDNAs using mito-mice with hearts carrying 88% mutant Delta mtDNA4696 with a 4696 deletion. COX histochemistry, quantitative PCR analysis, and electronmicrographs showed that accumulation of 91.6% Delta mtDNA4696 in single cardiac muscle fibers induced progressive reduction of COX activity to form COX-negative fibers. Moreover, hearts carrying 88% Delta mtDNA4696 consisted of three types of cardiac muscle fibers with different functional properties, COX-positive, -negative, and -intermediate fibers, which corresponded respectively to three types of fibers with different structural properties; type A fibers containing mitochondria with only lamellar cristae, type B containing mitochondria with only tubular cristae, and type C possessing mitochondria with both lamellar and tubular cristae. These observations suggest that lamellar cristae with COX activity transform into tubular cristae without COX activity along with the accumulation of Delta mtDNA4696, which would be responsible for insufficient supply of mtDNA products required to keep the normal structure and function of mitochondrial cristae. The correlation of these structural and functional abnormalities of cristae should provide important insight into diagnosis of cardiomyopathies caused by accumulation of pathogenic mutant mtDNAs.