Objective　To explore the clinical characteristics, diagnosis and treatment of Leigh syndrome with pyruvate dehydrogenase complex E1 α subunit deficiency caused by PDHA1 gene mutation. Method　Two boys visited doctors because of psychomotor retardation. Leigh syndrome was suggested by magnetic resonance imaging (MRI) and confirmed by biochemical metabolism and genetic tests. The clinical data were retrospectively analyzed. Results　Two boys visited a doctor at the age of 13 month and 4 months respectively for mental retardation, dystonia and muscle weakness at the age of 13 months and 4 months respectively. Brain MRI revealed symmetrical lesions in bilateral basal ganglia. Serum pyruvic acid and lactic acid levels increased significantly, while blood amino acid and acylcarnitine profiles were normal. Genetic analysis revealed missense mutations in the X chromosome PDHA1 gene , c.615C>G and c.605A>G, in the two boys respectively, which were new mutations never reported. Therefore, the two boys were diagnosed with Leigh syndrome caused by pyruvate dehydrogenase complex E1 α subunit deficiency. Conclusion　The clinical manifestations of PDHA1 gene mutation in children are complex and varied. The possibility of mitochondrial disease should be considered in children with developmental retardation of unknown cause. Gene detection is helpful for diagnosis, treatment and genetic counseling.