Mutations in mitochondrial DNA (mtDNA) are a major cause of hearing loss. In this study, we performed a systematic mutational screening of the 12S rRNA, tRNA Ser(UCN), tRNA Lys and tRNA Leu(UUR) genes in 227 unrelated patients with nonsyndromic hearing impairment for the first time in a Korean population. We found two individuals with an A1555G mutation, which is a frequency (0.9%) lower than that of other East Asians. Furthermore, two novel variants (C895T and 961-CC insertion) in the 12S rRNA gene were identified in the affected individuals, but were absent in 217 controls, indicating that they may play a role in the pathogenesis of hearing loss. Notably, 961delT and T1005C mutations were identified at similar frequencies in both patients and control subjects. Our data suggest that these variants seem to be polymorphisms rather than causes of disease. On the other hand, we did not find any of the known deafness-associated mutations in these tRNA genes. These data suggest that the 12S rRNA gene may be a hot spot for mitochondrial mutations causing hearing loss in the Korean population.