The characterization of peptide bound to major histocompatibility complex (MHC) molecules has yielded insight to certain functional aspects of MHC molecules, the effects of MHC polymorphism, and the mechanism of antigen processing and presentation. The self-peptides bound to over 20 different human MHC molecules have been structurally analyzed, and they reveal information that complements our understanding of the three-dimensional structure of MHC molecules established by X-ray crystallography. Sequence analysis of individual self-peptides and the identification of their precursor proteins reveal the cellular geography of antigen processing and lays the foundation for advanced study of tolerance, autoimmunity, and anti-tumor immunity.