Mitochondrial diseases are clinical phenotypes associated with mitochondrial dysfunction, which can be caused by mutations of mitochondrial DNA (mtDNA) or of nuclear genes. Since there are no high-performance transfect systems yet to make particular mtDNA mutation, and tissue sources are limited by ethical issue and injury, the molecular pathogenesis of mitochondrial diseases remains poorly understood. The generation of induced pluripotent stem (iPS) cells from adult somatic cells has opened a remarkable avenue for theoretic study and therapeutic application. Patient-specific induced pluripotent stem cells and differentiated cells derived from them are attracting increasing attention to elucidate the mechanisms underlying mitochondrial diseases. In this review, we summarize the advances of iPS cells, advantages of patient- specific iPS cells as a novel disease model, especially in mitochondrial disease. Occurring challenges and perspectives of patient-specific iPS cells research are also discussed.