Class II antigens encoded within the major histocompatibility complex (MHC) have been examined at the ultrastructural level in enterocytes from both man and rat. A protocol has been developed for fixation which, in conjunction with a pre-embedding indirect immunoperoxidase technique preserves antigenicity of the class II molecules and allows detection of intracellular antigen. Details of the technique are provided and discussed in relation to the general paucity of information available on ultrastructural localization of class II MHC molecules. Class II MHC antigens have been identified on the basolateral cell membranes of enterocytes in both species and they have also been found in association with intracellular organelles that have the appearance of multivesicular bodies and secondary lysosomes. These observations link class II molecules with the endocytic pathway in enterocytes and suggest a possible role in the handling of gut antigens. The findings may have a more general significance in relation to the site of engagement between processed antigen and MHC molecules in specialized antigen-presenting cells.