Following organ transplantation many patients suffer from drug-related side effects, or receive more immunosuppression than necessary to prevent rejection. Hence, parameters are needed to tailor the immunosuppressive therapy to the individual needs of an organ recipient. The aim of this study was to determine whether drug combinations provoke specific gene expression patterns in a simple assay system in vitro. Stimulated peripheral blood lymphocytes were cultured in the presence of cyclosporine A, tacrolimus, mycophenolic acid, everolimus and sirolimus, or combinations thereof. Using a cDNA microarray, we found that all samples clustered in drug-specific groups. Gene expression profiles were almost identical in PBL treated with either cyclosporine A or tacrolimus, and with either sirolimus or everolimus. More than 50 genes were synergistically affected by combinations of calcineurin-inhibitors and TOR-inhibitors and drug-specific regulated genes could be identified for both substance groups. Our data suggest that in vitro gene profiling can be used to describe synergistic effects of immunosuppressive drugs. Furthermore, our approach may help to identify marker genes urgently needed to optimize and individualize immunosuppressive drug regimens after organ transplantation.