Renal manifestations of mitochondrial cytopathies have been described, but nephrotic syndrome with respiratory-chain disorders have been described extremely rarely. We report a 9-month-old boy with a mitochondrial cytopathy preceded by a 2-month history of steroid-resistant nephrotic syndrome. Percutaneous renal biopsy revealed diffuse mesangial sclerosis, and mutational analysis was compatible with PLCE1 mutation. However, electron microscopic findings of renal tissue, sensorineural hearing loss, and other ocular and neurologic findings led us to suspect mitochondrial cytopathy. Muscle tissue analysis showed a deficiency of the respiratory chain complex IV. The clinical presentation of our patient is not typical for primary cytochrome oxidase (COX) deficiency but showed similarities with patients carrying AR mutations in COX10. This was the first case in the literature with both PLCE1 mutation and COX deficiency. We could not identify pathogenic mutations in the COX10 gene, suggesting that PLCE1 deficiency could be the cause of the secondary deficiency of COX. Another, more likely, possibility is that the mitochondriopathy phenotype is caused by another mutation homozygous by descent in a yet unidentified recessive gene.