Mutations occur in mitochondrial DNA (mtDNA) in a strand-asymmetric manner. The suppressed usage of cysteine residues in the H-strand-encoded subunits can be ascribed to the mutational instability of the codon for cysteine. The usage of cysteine was suppressed even in the L-strand-encoded ND6 subunit in which the codon for cysteine was stable. Survey of the entire sequences of mtDNA from 43 individuals revealed three amino acid replacements creating cysteine residues. A patient with fatal infantile cardiomyopathy carried a mutation causing a Tyr-->Cys replacement along with three tRNA mutations. A patient with hypertrophic cardiomyopathy carried two mutations causing a Ser-->Cys replacement and a Tyr-->Cys replacement besides two tRNA mutations. The gain of cysteine residues might accelerate the inactivation of the subunits either by reactive oxygen species or by lipid-peroxidation products, and this gain, possibly in association with tRNA mutations, can be a genetic risk factor for degenerative diseases.