When microorganisms invade the body, they encounter a large asssortment of defense mechanisms. Among these, phagocytes play an important role in the process of killing pathogens. This event is mediated by two important processes, viz. activation of the NADPH oxidase enzyme, which leads to the production of toxic oxygen metabolites, and fusion of intracellular granules with the phagosome (the vesicle that contains the ingested micro-organisms), which causes release of the toxic granule contents into this vesicle. The human NADPH oxidase is a very complex enzyme, in two ways: 1. it exists of at least 6 components: cytochrome b558 (a heterodimer comprised of gp91-phox and p22-phox), p47-phox, p67-phox, p40-phox, rac and Rap1A, and 2. there are multiple signal transduction pathways leading to activation of the NADPH oxidase. The most likely reason for this complexity is the toxicity of the oxygen radicals produced by the active NADPH oxidase; these compounds are not only harmful to the invading pathogens, but also to the surrounding tissues. This latter effect is enforced by the activation of metalloproteases released by neutrophils and by oxidation of protease inhibitors by oxygen metabolites. Therefore, an improper activation of the NADPH oxidase must be prevented at all costs and, when the infection has been cleared, a rapid deactivation mechanism is imperative. In this review, the interaction between the different components of the NADPH oxidase and the activation of these proteins will be discussed.