A new point mutation at nucleotide pair 3291 in the mitochondrial tRNA-Leu(UUR) gene was found in a Japanese MELAS patient. The nucleotides at the mutated site were evolutionarily invariant from humans through sea urchins. The mutant genomes were detected in a heteroplasmic fashion in muscle and blood cells of the proband by means of PCR-RFLP. Among 46 MELAS, 5 MERRF, 23 CPEO and 55 normal controls examined, this is the only patient with the mutation. This is the third mutation associated with MELAS in addition to nucleotides at 3243 and 3271. All three mutations occurred within the tRNA-Lue(UUR) region indicating that the tRNA alteration is responsible for the MELAS phenotype.