Focal segmental glomerular sclerosis (FSGS) is known as one of major renal complication of mitochondrial cytopathies. Glomerular epithelial cells are primary pathogenic sites in FSGS lesions. Glomerular epithelial cells are regarded as terminally differentiated cells and do not proliferate. This characteristic is the same for neuron cells and muscular cells, which are major sites of mitochondrial DNA mutations accumulation. Accumulation of mitochondrial DNA mutations might induce mitochondrial dysfunction and lead to FSGS lesion in glomeruli or these accumulations are only consequences of pathogenic stimuli to glomerular epithelial cells during the disease course of several glomerulopathies. Further investigations are needed to clarify pathogenic role of mitochondria and mitochondrial DNA mutations.