The presentation of pathogen-derived peptides on major histocompatibility complex (MHC) class I molecules of infected cells is a crucial step in host defense that initiates the adaptive cellular immune response and controls the expansion and effector function of pathogen-specific T cells. It is especially important in the defense against noncytopathic viruses, such as the hepatitis C virus (HCV), that reside and amplify intracellularly and cannot be completely cleared by the humoral arm of the immune response alone.Although MHC class I loci are among the most polymorphic and variable genes in the genome (38), certain common features that determine the nature of binding peptides have been identified. First, the peptide-binding site is formed by two parallel ␣-helices on top of antiparallel oriented -strands. The MHC class I binding groove allows binding of peptides 8 to 11 amino acids in length. Second, the specificity of binding is determined by polymorphic amino acid residues in the ␣1 and ␣2 domains whose side chains protrude into the peptide-binding groove. Third, based on these residues, certain MHC supertypes have been defined that bind peptides with the corresponding binding motif, i.e., specific anchor amino acid residues that interact with the polymorphic complementary pockets of the MHC peptide-binding grooves (54).The chimpanzee is an important animal model for studying infections with HCV, human immunodeficiency virus (HIV), malaria, and other pathogens and for evaluating candidate vaccines. Several relevant vaccination strategies aim at the induction or enhancement of cellular immune responses against viral epitopes that are presented by common human MHC alleles. Although chimpanzee MHC alleles are closely related to human alleles, distinct differences do exist. For example, the chimpanzee Patr-A locus is less polymorphic than the human HLA-A locus (35). In addition, all known Patr-A alleles appear to be related to only one of the two sublineages of HLA-A alleles, namely to the HLA-A3 lineage, which comprises the HLA-A1, -A3, -A9, -A11, and -A80 family (15,31,34,35,45); a specific Patr lineage or allele related to the most frequent human allele, HLA-A2, has not been identified at the molecular level. Moreover, it is not known whether those HCV epitopes that are well characterized in HCV-infected patients and therefore represent promising vaccine candidates (4,6,9,40) are also endogenously processed and recognized by T cells of HCV-infected chimpanzees.