Endogenous antigens are those being produced within cells of the body. Examples include proteins from replicating viruses, proteins from intracellular bacteria, and tumor antigens. The body marks infected cells and tumor cells for destruction by placing peptide epitopes from these endogenous antigens on their surface by way of MHC-I molecules. Cytotoxic T-lymphocytes (CTLs) are then able to recognize peptide/MHC-I complexes by means of their T-cell receptors (TCRs) and CD8 molecules and kill the cells to which they bind.

1. Endogenous antigens, such as viral proteins, pass through proteasomes where they are degraded into a series of peptides.
2 & 3. The peptides are transported into the rough endoplasmic reticulum (er) where they bind to the grooves of newly synthesized MHC-I molecules.
4. The endoplasmic reticulum transports the MHC-I molecules with bound peptides to the Golgi complex which, in turn, transports them to the cytoplasmic membrane where they become anchored. Here, the peptide and MHC-I complexes can be recognized by CTLs by way of TCRs and CD8 molecules having a complementary shape.