The NADPH oxidase of phagocytic cells of the immune system plays an important role in the destruction of certain types of microbial pathogens during infections. Its inappropriate activation to release reactive oxidants may also contribute to host tissue damage in inflammatory diseases. In this review, the structure of the NADPH oxidase is described and many of the commonly used methods to detect its activation during the respiratory burst are listed. The advantages and disadvantages of each of these methods are critically discussed.