Heart transplantation (HT) remains the treatment of choice for advanced chagasic cardiomyopathy. New immunosuppression protocols have provided better control of rejection (RJ) and cardiac allograft vasculopathy. However, their influence on infection and Chagas disease reactivation (CDR) is not well established. The aim of this study was to compare the CDR rate in patients under two different immunosuppression protocols. We studied 39 chagasic patients who had undergone orthotopic HT between April, 1987 and June, 2004. They were divided into two groups, one taking azathioprine (group 1=24 patients) and the other taking mycophenolate mofetil (group 2=15 patients), in the standard doses (2 mg/kg/day and 2 g/day, respectively), beside prednisone and cyclosporine, in equivalent doses. The number of CDR and RJ episodes were analyzed in the first and second years after HT. CDR rates were 8%+/-5% at 1 year and 12%+/-6% at 2 years of follow-up in group 1. Otherwise, patients in group 2 presented CDR rates of 75%+/-10% and 81%+/-9% at the same periods, respectively (p<0.0001, hazard ratio=6.06). When comparing RJ rates in the first year after HT, both groups had similar behavior under both immunosuppression protocols (p=0.88). These data show that current prescribed doses of mycophenolate mofetil increase the early risk of CDR without changing RJ incidence in this period.