This study aimed to define the molecular mechanism during induction of spontaneous liver transplant tolerance using microarrays and to focus on molecular pathways associated with tolerance by meta-analysis with published studies. The differences in the early immune response between PVG to DA liver transplant recipients that are spontaneously tolerant (TOL) and PVG to Lewis liver transplants that reject (REJ) were examined. Spleens from TOL and REJ on days 1 and 3 were compared by 2 color microarray. Forty-six of 199 genes differentially expressed between TOL and REJ had an immunological function. More immune genes were increased in TOL vs. REJ on day 1, including STAT-1, IRF-1 and complement C3. Differential expression of selected genes was confirmed by quantitative RT-PCR. The results were compared to two published high-throughput studies of rat liver transplant tolerance and showed that C3 was increased in all three models, while STAT-1 and IRF-1 were increased in two models. The early increases in immune genes in TOL confirmed previous reports of an active early immune response in TOL. In conclusion, the increase in STAT-1, IRF-1 and complement component C3 in several models of liver transplant tolerance suggests that the STAT-1/IRF-1 apoptotic pathway and C3 may be involved in the tolerogenic mechanism. Liver Transpl 12: [636][637][638][639][640][641][642][643] 2006 Despite their ability to prevent acute rejection episodes, conventional immunosuppressive drugs are less successful for control of chronic rejection, increase susceptibility to infections and carcinoma, and have been linked to post-transplant diabetes and renal tubular atrophy. These limitations, along with their expense, have driven development of new drug-free or drug-minimizing specific immune tolerance therapies. One approach is to study animal models of transplant tolerance. Perhaps the most powerful of these is the rat liver model, in which livers transplanted across complete MHC barriers are accepted long-term by the recipient without the requirement for immunosuppression and rapidly induce tolerance to subsequent donor-strain skin grafts.