The techniques of classical epifluorescence microscopy are already widely used by the immunological community to detect antigens at the cellular level. Coupled with the use of specific inhibitors that affect diverse intracellular events, these techniques have provided valuable information on the mechanisms involved in antigen presentation. The same biological samples can now be examined by confocal microscopy, which has a higher resolution than conventional microscopy and allows one to analyse quantitatively single cross-sections of the sample. The confocal microscope is therefore especially well-suited for studies on intracellular membrane traffic, cell-to-cell interactions, and the distribution of particular antigens and their co-localization with other intracellular markers. This review describes the technique of confocal microscopy and the goals of sample preparation, along with several detailed protocols for fixing and permeabilizing cells and mounting them on microscope slides. Representative examples are cited from studies on the endocytosis of surface receptors, the distribution of adhesion and major histocompatibility complex (MHC) molecules, and the interaction of an intracellular parasite with MHC molecules of the host cell.