The formation of microbicidal oxidants by stimulated phagocytes is a major mechanism of host defence against infection and may also cause unwanted damage to host tissues in the setting of inappropriate inflammation. Recently, the molecular basis for oxidant production has been defined by elucidating the structure, biochemistry and regulation of the phagocyte NADPH oxidase, a multicomponent enzyme that uses NADPH to reduce molecular oxygen to superoxide anion which is then converted to hydrogen peroxide. Many of the advances resulted from the study of phagocytes obtained from patients with inherited abnormalities of the NADPH oxidase system, known as the chronic granulomatous diseases of childhood (CGD). These patients are susceptible to life-threatening infections. The NADPH oxidase is a complex enzyme system that has been shown to contain cytosolic and membrane components that assemble at the plasma membrane with cell activation. These components include a membrane NADPH-binding flavoprotein, cytochrome b558, the cytosolic proteins p47phox, p67phox and a small ras-related guanosine triphosphatase or rac protein that confers guanosine triphosphate sensitivity to the NADPH oxidase. Clinically, the NADPH oxidase system can be stimulated with interferon-gamma, resulting in reduced infections in patients with CGD. In addition, the recent incorporation of genes for the components of the NADPH oxidase into retrovirus vectors has resulted in successful transduction of these genes into blood stem cells from CGD patients with correction of the functional defect. This suggests that gene therapy for correction of CGD will be possible in the near future.