An important goal in transplantation is to tailor immunosuppression to the individual needs of the patient, avoiding both rejection and over-immunosuppression. Opportunistic infections and malignancies remain a significant cause of death after transplantation and are obvious consequences of over-immunosuppression. Currently, monitoring of immunosuppression is conducted mainly on the basis of pharmacokinetic characteristics, which do not necessarily predict clinical outcome in the individual. This review focuses on the potential of using biomarkers as a monitoring tool to prevent over-immunosuppression after transplantation. Clinical Pharmacology & Therapeutics (2011) 90 2, 316–322. doi:10.1038/clpt.2011.111