Dr. Madsen leads three interrelated research groups that study the molecular and cellular mechanisms of transplant rejection and immune tolerance in mice, swine and nonhuman primates, respectively. By understanding the biological of these processes Madsen hopes to find ways to prolong organ allograft survival (inducing tolerance), extend transplant recipients lives (preventing chronic rejection) and increase the organ donor pool (pig-to-human xenotransplantation).

Dr. Madsen's laboratory has been the first to induce long term tolerance of cardiac allografts in large animals and to demonstrate the natural killer cells contribute to cardiac allograft vasculopathy. He has been continuously funded by the NIH since 1995.

In 2002, he received the Fujisawa Basic Science Award from the American Society of Transplantation. In 2005, he was made the W. Gerald and Patricia R. Austen Distinguished Scholar in Cardiac Surgery at Massachusetts General Hospital. In 2009, he was elected president of the American Society of Transplantation.