The phagocyte NADPH oxidase is a key component of the innate immune response against invading microorganisms, because the generation of superoxide (O(2)(-)) inside the phagocytic vacuole by this enzyme is responsible for microbial killing by mechanisms that are directly or indirectly dependent on reactive oxygen species (ROS) formation. Most of what is known about the membrane-embedded and cytosolic NADPH oxidase subunits and their intricate network of interactions on assembly and activation has been derived from biochemical and biophysical studies involving subcellular fractionation or reconstituted cell-free systems. Such investigations can be complemented by single-cell microscopy on phagocytes, which may reveal spatial and/or temporal details about NADPH oxidase assembly that cannot be obtained from fractionated-cell assays. In recent years, we have investigated the NADPH oxidase in neutrophils using two complementary optical imaging techniques: Raman microscopy, a vibrational spectroscopic technique that does not require protein labeling, and live-cell fluorescence microscopy, which sheds light on the dynamics of NADPH oxidase assembly in individual cells. Here, we briefly introduce these techniques, compare their characteristics, and show their potential for studying NADPH oxidase at the single-cell level. New microscopy data are presented to illustrate the versatility of Raman and fluorescence microscopy on intact neutrophils.