Superoxide is instrumental in the killing of microorganisms by phagocytic cells. It is generated by the NADPH oxidase system, a membrane-bound electron transport complex which pumps electrons from NADPH in the cytoplasm across the wall of the phagocytic vacuole to molecular oxygen. Superoxide deficiency results in the genetically inherited condition Chronic Granulomatous Disease (CGD), in which the patient is abnormally susceptible to infection. In recent years many of the underlying genetic defects in CGD have been identified and are providing important insights into the structure and mechanism of the NADPH oxidase complex.