Mammalian SCO1 and SCO2 are evolutionarily-related copper-binding proteins that are required for the assembly of cytochrome c oxidase (COX), a mitochondrial respiratory chain complex, but the exact roles that they play in the assembly process are unclear. Mutations in both SCO1 and SCO2 are associated with distinct clinical phenotypes as well as tissue-specific COX deficiency, but the reason for such tissue specificity is unknown. We show in this study that although both genes are expressed ubiquitously in all mouse and human tissues examined, surprisingly, SCO1 localizes predominantly to blood vessels, whereas SCO2 is barely detectable in this tissue. To our knowledge, SCO1 is the first known example of a mitochondrial protein that is strongly expressed in the vasculature. We also show that the expression of SCO1, but not of SCO2, is very high in liver (the tissue most affected in SCO1-mutant patients), whereas the reverse holds true in muscle (the tissue most affected in SCO2-mutant patients). Our findings may help explain the differences in clinical presentations due to mutations in SCO1 and SCO2 and provide clues regarding the partially nonoverlapping functions of these two proteins.