Mitochondrial disorders have notoriously variable clinical presentations, particularly in children. A growing number of reports describe mutations in the mitochondrial DNA (mtDNA)-encoded subunits of complex I (EC 18.104.22.168) causing early-onset encephalopathy. Here, we describe two Korean siblings with childhood-onset progressive generalized dystonia and one Korean child with strokelike episodes in infancy; all three had bilateral lesions of the basal ganglia and partial deficiencies of complex I. Analysis of their mtDNA revealed a novel heteroplasmic m.10197G>A mutation (A47T) in the ND3 (NADH dehydrogenase subunit 3) gene. This study underscores the importance of screening mtDNA-encoded respiratory chain structural genes, including ND3, in pediatric patients with unexplained encephalopathies.