To better comprehend the thymic microenvironment, it is necessary to identify the antigenic profile of cortical thymic epithelial cells (cTECs) that are involved in the development of major histocompatibility complex (MHC)-restricted T cells. Ultrastructurally, cTECs can be classified into four morphologically distinct subtypes: subcapsular/perivascular (EC1), pale (EC2), intermediate (EC3) and dark (EC4) cells. Several immunohistochemical studies were done on cTECs at the light and electron microscopic levels, but not with reference to the above subtypes. In the present paper, we analysed the expression of MHC class II antigen and cathepsin L by individual cTEC subtypes at the electron microscopic level. We show that (1) MHC class II antigens are expressed on the cell surfaces except on the basal surface of EC1, both on the cell surface and in intracytoplasmic vacuoles of EC2, and only in the intracytoplasmic vacuoles of EC3 and EC4, and (2) that cathepsin L is expressed strongly and uniformly throughout the cytoplasm of EC2, but weakly and non-uniformly in the cytoplasm of EC1, EC3 and EC4. These results show that MHC class II antigen expression and cathepsin L expression is heterogeneous in cTEC subtypes and suggest that EC2 might play a significant role in the development of CD4+ T cells.