The superoxide-producing phagocyte NADPH oxidase is activated during phagocytosis to destroy ingested microbes. The adaptor protein p40(phox) associates via the PB1 domain with the essential oxidase activator p67(phox), and is considered to function by recruiting p67(phox) to phagosomes; in this process, the PX domain of p40(phox) binds to phosphatidylinositol 3-phosphate [PtdIns(3)P], a lipid abundant in the phagosomal membrane. Here we show that the PtdIns(3)P-binding activity of p40(phox) is normally inhibited by the PB1 domain both in vivo and in vitro. The crystal structure of the full-length p40(phox) reveals that the inhibition is mediated via intramolecular interaction between the PB1 and PX domains. The interface of the p40(phox) PB1 domain for the PX domain localizes on the opposite side of that for the p67(phox) PB1 domain, and thus the PB1-mediated PX regulation occurs without preventing the PB1-PB1 association with p67(phox).