Cockayne syndrome (CS) is a rare autosomal recessive disease with progeroid symptoms, which is caused mainly by mutations in the CS genes CSA and CSB. Although the relevance of mitochondria in the aging process is known for several decades, research focused primarily on the role of the CS proteins in the nucleus. Recently, however, mitochondrial contribution to aging-associated symptoms of CS has been described. Inside mitochondria, CS proteins have roles, which partially differ from their nuclear functions. Up to now it is known that mitochondrial CS proteins are associated with base excision repair (BER) and transcription of mitochondrial DNA. However, it has been hypothesized that these are not the only functions of mitochondrial CS proteins as the occurrence of mutations like the common deletion are in need of separate explanations.