The endocytic and phagocytic pathways are composed of a series of vesicular or vacuolar organelles within the cytoplasm in which exogenous proteins or particles are processed. This processing includes catabolism of protein antigens by proteases that exist within endosomes, lysosomes, phagosomes, and phagolysosomes. Antigen processing produces peptides that bind to class II MHC (MHC-II) molecules, which also target to vesicular compartments. Multiple different vesicular compartments may contribute to antigen processing, although some compartments appear to be specialized in order to perform certain antigen processing functions. The relative levels of MHC-II molecules, processing enzymes, and other specialized molecules (e.g., HLA-DM) are among the variables that determine the relative contribution of different compartments. Recent studies have begun to identify specific compartments that mediate certain antigen processing functions, including the binding of immunogenic peptides to MHC-II molecules.