At least three proteins, COX17p, SCO1p, and its homologue SCO2p are thought to be involved in mitochondrial copper transport to cytochrome-c-oxidase (COX), the terminal enzyme of the respiratory chain. Recently, we and others have shown that mutations in SCO2 are associated with a lethal infantile hypertrophic cardiomyopathy (HCMP) with COX-deficiency. The majority of patients with a similar phenotype were, however, negative for SCO2 mutations, suggesting the other genes as candidates for this disorder. Here we report on the genomic organization of SCO1 and COX17 on human chromosomes 17 and 3 respectively, and the complete sequence analysis of COX17 and SCO1 in 30 patients with COX deficiency. Using a panel of human:mouse-monochromosomal hybrids, the expression of COX17 was specifically restricted to chromosome 3, indicating that the previously reported sequence on chromosome 13 represents a pseudogene. DNA sequence analysis of SCO1 and COX17 in nine patients with severe COX deficiency and fatal HCMP, and in 21 patients with other COX deficiency disorders, did not reveal any pathogenic mutations or polymorphisms. We conclude that neither SCO1 nor COX17 are common causes of COX deficiency disorders.