Although recent advances in immunosuppressive therapy have dramatically enhanced the early survival of solid organ transplant recipients, acute rejection still occurs in some recipients. Long-term immunosuppressive drug administration, furthermore, entails a number of potentially significant problems such as infection, spontaneous neoplasm and drug toxicity. Alloantigen specific tolerance induction is the ultimate goal in transplant immunology, and can be induced in a rodent model; however, the precise mechanism by which specific tolerance is affected are not clearly understood, and the current immunosuppression regimens have all failed to achieve this goal in a clinical setting. DNA microarray technology has made it possible to analyze the expression of a large number of genes and revolutionized many areas of biology and medicine. This new technology can provide non-biased, global expressions of tens of thousands of genes simultaneously. Recent studies on gene expression profiles in various diseases, including allograft rejection, have successfully provided important information and new insights into the biological mechanisms of these diseases. In this article, we reviewed these insights, especially with the viewpoint of appliance of microarray technology to clinical solid organ transplantation.