Defects in phagocyte function or in the interactions between phagocytes, microorganisms and serum factors are associated with increased susceptibility to infection. Flow cytometry (FCM) offers rapid and reproducible measurements of single cells in suspension and, following staining with one or more fluorochromes, simultaneous biochemical and functional examinations of the complex process of phagocytosis. FCM techniques have been used for more than two decades to evaluate phagocyte cellular defects, as well as species-specific serum opsonic activities during disease and after vaccination. Recently, multiparameter assays have been developed to reveal the antigen-specificity of opsonophagocytic responses. This review presents basic methodological principles of FCM quantitation of phagocytosis and intracellular oxidative burst, and assays to evaluate species-specific and antigen-specific opsonophagocytosis. The calculations performed to present opsonophagocytosis results, as well as technical and methodological challenges are discussed, and examples of applications are presented.