A novel mutation in the mitochondrial tRNA(Thr) gene associated with a mitochondrial encephalomyopathy. A novel G-to-A transition at nucleotide 15915 in mtDNA is described. The patient showed a combination of muscle weakness, hearing loss, mental retardation, and seizures. Muscle biopsy showed RRFs and focal COX deficiency. We sequenced all mtDNA, and found 5 novel nucleotide substitutions. Three of them were synonymous mutations, one was a missense mutation in cytochrome b gene (A-->G at nt 15422), and the last one was the 15915 mutation in tRNA(Thr) gene. We screened for the 15422 and the 15915 mutations with mismatch primers and found that one of 104 normal individuals carried the former one and none of 175 had the latter one. The 15422 mutation existed in homoplasmic states both in the patient and the normal individual, suggesting that this is a polymorphism. In contrast the 15915 mutation resided in heteroplasmic states in muscle, skin fibroblast and blood. The nucleotide substitution at nt 15915 disrupts a highly conserved base pair in anticodon stem of the tRNA(Thr). Our data suggest that the 15915 mutation is an additional mtDNA mutation responsible for mitochondrial encephalomyopathies.