Although the role of the major histocompatibility complex (MHC) of the rat (RT1) in graft rejection has been established, the role of non-RT1 genes is not well understood. To investigate the influence of MHC and non-MHC genes in graft rejection, various combinations of congenic and inbred strains of rats were used as donors and recipients of skin grafts and perfused abdominal heart grafts. In addition, hemagglutinating and cytotoxic antibody responses were evaluated to assess loci that were serologically active in transplantation. Our results demonstrate that: (1) RT1 antigens are the most important determinant in heart and skin rejection; (2) antigens controlled by non-MHC genes also play a major role in rejection because they cause disparate heart grafts to be rejected by day 18 and skin grafts by day 26; (3) RT2 cell antigens alone do not cause graft rejection; and (4) allogeneic differences at the RT1, RT2, RT3, and RT6 loci elicit an antibody response in heart transplantation.