Chronic granulomatous disease (CGD) is a primary immunodeficiency that affects phagocytes of the innate immune system and is characterized by a greatly increased susceptibility to severe bacterial and fungal infections. CGD is caused by mutations in any one of four genes that encode the subunits of phagocyte NADPH oxidase, the enzyme that generates microbicidal (and pro-inflammatory) oxygen radicals. Of the 410 CGD mutations identified, 95% cause the complete or partial loss of protein and provide little information regarding the relationship between protein structure and function. The remaining 5%, however, result in normal levels of inactive protein and many have provided valuable insights into the function of affected subunits and their roles in oxidase regulation and catalysis. Moreover, recent CGD studies have revealed that recombination events between the p47-phox gene (NCF-1) and its pseudogenes not only cause the absence of p47-phox, but also predict the generation of a novel fusion protein.