Fundamental studies in solid organ transplantation have characterized specific functional roles for individual genes in the immunological cascade leading to organ rejection. Nevertheless, significant redundancy in the immune system is suggested by clinical variability in acute rejection outcomes, in the progression of chronic rejection, and by the potential to acquire graft tolerance. Underlying all of these complex systems are concordant expression and co-regulation of multiple genes in known and novel molecular pathways. Ascertaining their individual functions in adapting the effector response is now possible with gene expression profiling using microarrays. Although cDNA microarrays (large numbers of genes represented by complementary DNAs or oligonucleotides immobilized onto microscope slides or silicon chips) were successfully used to profile gene expression in cancer (15,16,17,18,19), their impact in transplantation research has so far been relatively modest.