Mitochondrial disease is an energy metabolic disorder with various organ involvement. Iron is widely known to be one of the most important nutriments required for normal brain development and several essential metabolic functions. We retrospectively studied the laboratory data on iron deficiency (ID) in 69 children with mitochondrial respiratory chain complex (MRC) defects by biochemical enzyme assay using muscle tissue. We analyzed the differences between groups of mitochondrial disease based on the presence of ID. ID has higher prevalence in children with mitochondrial disease than in the normal population. There were 6 (9%) patients with low hemoglobin, 12 (17%) with low serum ferrtin, and 22 (32%) with low transferrin saturation levels among children with MRC defects. In comparisons between the ID and the non-ID group of MRC-defect patients, the frequency of MRC I defect was significantly higher in the ID group while that of MRC IV defect was higher in the non-ID group. Abnormal brain magnetic resonance imaging (MRI) findings were more frequently detected in the ID group. The incidence of failure to thrive and gastrointestinal symptoms were significantly higher in the ID group. Early diagnosis and proper treatment of ID are recommended. Especially in cases with risk factors such as failure to thrive or gastrointestinal manifestation, active evaluation of ID should be encouraged.