Abstract: 　Objective　To explore the clinical and molecular-genetic features and prognosis of mitochondrial encephalopathy in children. Methods A total of 11 patients diagnosed with mitochondrial encephalopathy were collected from 2008 to 2013 in Chinese PLA General Hospital, Department of Pediatrics. The clinical manifestations, laboratory tests, muscle pathology and mitochondrial gene sequencing in patients were analyzed and followed-up. Results The onset age of the patients ranged from 6 months to 12 years with the duration of disease from 2 months to 3 years. Of the 11 patients, 6 cases were diagnosed with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), 5 cases with mitochondrial disorder induced by mitochondrial respiratory chain enzyme deficiency. Main manifestations included convulsions, vomiting, headache, mental retardation, paralysis, etc. 10 patients had elevated lactate, and 7 patients had elevated pyruvate; 6 cases showed increased slow wave in EEG background; Cranial MRI showed the damage involved in bilateral basal ganglia in 2 cases, temporal and occipital lobes in 3 cases, , multiple lesions in 2 cases, frontal and parietal occipital lobes in one patient and hypothalamus in one patient; 3 patients were underwent MRA examination, 2 cases were normal, the other showed less shunts in contralateral left artery in the brain; 3 cases who underwent MRS showed lactate peak. 2 cases of children underwent skeletal muscle biopsy, and one case showed abnormal mitochondria accumulation. Mitochondrial respiratory chain complex (I~V) defects test showed complex IV defects in 2 cases, complex V defects in 1 case, and combined defects of complex I+III in 2 case. 5 cases were found with mitochondrial DNA mutations in different sites of white blood cells including T8993G, T8993C, A3243G and 11,777 mutations. Conclusions Clinical manifestation of mitochondrial encephalopathy in children is strongly heterogeneous. Laboratory tests, brain imaging, gene mutation and respiratory chain enzyme examination can help to make early diagnosis and treatment. These diseases have poor prognosis.