Some intracellular pathogens avoid killing within phagosomes--which are specialized microbicidal organelles in cells of the innate immune system--by altering phagosomal maturation or by entering a different subcellular compartment. The fate of the microorganisms is ultimately dictated by the composition of the surrounding environment. The unique problems associated with in situ measurements of intracellular microenvironments within intact cells and the advantages of quantitative fluorescence microscopy have recently been investigated. Of particular interest are the various techniques and reagents used in analysis of the pH and reactive oxygen intermediates in phagosomes and invasion vacuoles.