We present a patient with non-syndromic and sensorineural hearing impairment with a novel mitochondrial DNA transition. A 7-year-old boy showed progressive deafness. He gradually lost his hearing ability and his hearing function did not improve with hearing aids. Laboratory data revealed normal blood lactate and pyruvate levels. Genetic analyses for mitochondrial DNA and GJB2 and GJB6 genes were performed. Mitochondrial genes analysis revealed a novel heteroplasmic nucleotide substitution, m.628C>T, in the phenylalanine transfer RNA gene. This case study reveals m.628C>T transition as a novel mitochondrial nucleotide change which may be important in mitochondrial deafness.