Isolated cytochrome c oxidase (COX) deficiency (MIM#220110) is a relatively common biochemical finding in pediatric patients with mitochondrial disorder. It has been associated with different clinical phenotypes ranging from isolated myopathy to severe multisystem disorder. It is a genetically heterogeneous trait, and the most frequent genetic defects affect SURF1 and SCO2, two genes required for COX assembly. However, a significant proportion of patients lacks mutation in these genes and in other known genes that require COX biogenesis. COX18 is a novel COX assembly gene required for membrane insertion of the C-terminal portion of COX subunit II. We have studied 29 pediatric patients with isolated COX deficiency in the skeletal muscle associated with different clinical phenotypes. Mutations in SURF1, SCO2, SCO1, COX10, COX15 and in mitochondrial DNA, had been ruled out earlier. The COX18 gene was analyzed using a PCR-single-stranded conformation polymorphism (PCR-SSCP) protocol, and in 15 patients, the analysis was repeated by direct sequencing. No pathogenic mutations were detected in our cohort of patients indicating that COX18 mutations may be very rare or associated with other phenotypes than isolated COX deficiency in infancy.