The authors sequenced the entire mitochondrial DNA coding region in a group of 19 patients with non-arteritic anterior ischemic optic neuropathy (NAION) and in 100 controls. Synonymous and nonsynonymous nucleotide changes were more common in NAION patients (p < 0.001). Twelve of these (11 novel) were potentially pathologic, nine of which altered moderately or highly conserved amino acids in the functional domain of the affected protein. Mitochondrial malfunction may be a risk factor for NAION.