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We report the case of a patient born with extreme muscle hypotonia, respiratory failure, and slightly elevated serum levels of lactic acid. Histochemical examination and mitochondrial respiratory chain enzyme activities of a muscle biopsy specimen revealed reduced activities of complexes Ⅰ, Ⅲ, and Ⅳ, diagnostic of mitochondrial respiratory chain disorder. Hypertrophic cardiomyopathy developed as a complication and additional therapy was administered at 3 months after birth. He was able to be discharged to home on applied home mechanical ventilation with tracheotomy at 1 year old. The patient survived until 4 years and 10 months of age, upon which he died of bronchitis. Early-onset mitochondrial respiratory chain disorder shows very poor prognosis and long-term survival has not been reported. Prompt assessment of mitochondrial respiratory chain enzyme activities is necessary for the diagnosis of congenital nonspecific multiple-organ failure, and early intervention may achieve better prognosis for mitochondrial respiratory chain disorder.