The final steps in the production of adenosine triphosphate (ATP) in mitochondria are executed by a series of multisubunit complexes and electron carriers, which together constitute the oxidative phosphorylation (OXPHOS) system. OXPHOS is under dual genetic control, with communication between the nuclear and mitochondrial genomes essential for optimal assembly and function of the system. We describe the current understanding of the metabolic consequences of pathological OXPHOS defects, based on analyses of patients and of genetically engineered model systems. Understanding the metabolic consequences of OXPHOS disease is of key importance for elucidating pathogenic mechanisms, guiding diagnosis and developing therapies.