The primary immunologic barrier to overcome before clinical xenotransplantation can be successful is rejection mediated by preformed natural antibodies in the host, directed toward a single carbohydrate epitope Galalpha1-3Galbeta1-4GlcNAc-R (alphaGal) present on porcine tissue, encoded for by the enzyme glucosyltransferase UDP galactose:beta-D-galactosyl-1, 4-N-acetyl-D-glucosaminide alpha(1-3)galactosyltransferase (EC 2.4.1. 151) or simply alphaGT. Although we have shown previously that a gene therapy approach could be used to prevent production of natural antibodies specific for alphaGal, the ability to induce and maintain tolerance after rigorous antigen challenge would be required if similar approaches are to be used clinically. Here, we demonstrate in alphaGT knockout mice (GT(0) mice), which, like humans, contain in their serum antibodies that bind alphaGal, that the efficient transduction and expression of a retrovirally transduced alphaGT gene in bone marrow-derived cells induces stable long-term tolerance to the alphaGal epitope. GT(0) mice reconstituted with alphaGT-transduced bone marrow cells were unable to produce antibodies that bind alphaGal after extensive immunization with pig cells. Furthermore, using ELISPOT assays, we were unable to detect the presence of B cells that produce alphaGal reactive antibodies after immunization, suggesting that such B cells were eliminated from the immunologic repertoire after gene therapy. Interestingly, after tolerance to alphaGal is induced by gene therapy, the antiporcine non-alphaGal humoral response changes from a predominantly IgM to an IgG response. This suggests that once the natural antibody barrier is eliminated by the induction of tolerance, the antipig response changes to a typical T-cell-dependent response involving isotype switching. Thus, gene therapy approaches may be used to overcome immunologic responses leading to xenograft rejection, and similar gene therapy approaches could be used to overcome autoimmunity.