A 5-year-old child with clinical and radiologic evidence of Leigh syndrome (LS) showed a T-->C mutation at position nt 8993 in the mitochondrial DNA (instead of the more common T-->G substitution), resulting in an amino acid change from a highly conserved leucine to proline in subunit 6 of mitochondrial ATPase. The mutation was heteroplasmic and maternally inherited, and was present in high percentages in multiple tissues. This finding documents genetic heterogeneity of the ATPase 6 gene mutation associated with LS.