BackgroundMitochondria are the energy producing organelles practically in every human cell except erythrocytes. Indeed mitochondria are widespread in high energy requiring organs like brain, heart and muscles. Currently there are no clinical trials supporting with clear evidence which is the most suitable surgical or anesthetic management of a patient with known mitochondrial disease presenting with surgical disorders. This condition poses possible hazardous problems to the medical attention of those patients.Case presentationA case of an 8 year old child with known Electron Transfer Flavoprotein Dehydrogenase deficiency (ETFDH deficiency) requiring surgery for acute appendicitis is presented. Our approach for anesthesia revealed a combination of fentanyl, low dose propofol and nitrous oxide.ConclusionThe choice of the safest pharmacological anesthetic agents for patients with ETFDH deficiency is challenging given that most of the general anesthetic medications have multiple effects on mitochondria, fatty acids metabolism and striated muscles. Anesthetists are expected to individualize anesthetic care for the patient based on current publications for similar cases, medical history and knowledge of pharmacology and physiology.