The evolving era of functional genomics in organ transplantation is supported by advances in gene profiling, sequencing, proteomics, antibody profiling and bioinformatics, thus heralding a new era of intelligent and customized monitoring and therapy. These advances will serve to meet the critical unmet needs of improving graft survival, limiting graft injury from under-immunosuppression and reducing patient morbidity from over-immunosuppression. This review is a summary of current status of potentially useful technologies available for genomics and proteomics applications in transplantation with the emphasis on addressing the complexities of cellular immunology at the molecular level and the clinical challenges of transplantation today.