The availability of genomic sequencing for inherited diseases provides a more complete molecular basis for how an individual's genetic landscape influences clinical outcome. We describe a family where exome sequencing of a 3‐year‐old boy with clinical features of Cockayne syndrome (CS) confirmed the diagnosis of CS. He also had a mutation consistent with a pre‐symptomatic second disease, multiple endocrine neoplasia type 1 (MEN1), each potentially affecting multiple organ systems, in addition to a poorly defined variant in fumarate hydratase (FH). Genomic sequencing may reveal coexisting pathogenic mutations and variants which complicate clinical interpretation.