There is evidence that T cells can “directly” recognize intact allo-MHC molecules on the surface of allogeneic stimulator or target cells, and/or “indirectly” recognize processed allo-MHC peptides presented by self antigen-presenting cells (APCs). We and others have recently demonstrated that in vivo-primed rat CD4+ T cells recognize and proliferate to specific polymorphic amino acid sequences when presented as MHC allopeptides by self APCs. Studies on the mechanisms of indirect T cell recognition of alloantigen are now reported. First, we studied the immunogenicity of 4 synthetic polymorphic class II MHC allopeptides representing full-length sequences of the hypervariable domains of RT1. D u β (DR or IE-like) in several responder strains: LEW (RT1 1), ACI (RT1 a), BUF (RT1 b), BN (RT1 n), and control syngeneic WF (RT1 u) strains. Immunogenicity of the individual 25mer allopeptides varied in the different responder strains, indicating that self-restricted T cell recognition of allo-MHC peptides is determined not only by polymorphisms, but also by the responder MHC genotype.