BACKGROUND Current practice recommends that immunosuppressed patients (pts) receive yearly influenza (flu) vaccinations. However, disparity exists between current recommendations and clinical practice regarding the decision to administer flu vaccinations to heart transplant (Tx) pts. The purpose of this study was to examine the common clinical practices and outcome characteristics in Tx pts in a multi-institutional database. We assess the incidence of rejection, infection and flu in the months after administration of flu vaccinations. METHODS Between 1990 and 2001, 5,581 pts underwent Tx at 28 institutions. Pts who were >1 year post-Tx as of January 1, 2002 (N = 3,601) constituted the study group. RESULTS During the years 2002 and 2003, 89% of the institutions administered flu vaccines, with 7 institutions requiring pts to be >3 months (N = 1), 6 months (N = 1) and 12 months (N = 5) post-Tx. All 25 centers that vaccinated pts used trivalent inactivated vaccines during the months of October through January. Three centers did not vaccinate Tx pts due to a purported association with increased allograft rejection. There were no significant differences in the total number of rejection episodes (0.4% vs 0.3%, p = 0.7), rejection episodes by month (January: 0.4% vs 0%, p = 0.2; February: 0.5% vs 1.5%, p = 0.08; March: 0.5% vs 0%, p = 0.14), all infections (0.7% vs 0.6%, p = 0.6) and viral infections (0.1% vs 0%, p = 0.17) between centers that administered flu vaccines and those that did not, respectively. The incidence of flu was low in both groups. CONCLUSIONS Flu vaccinations can be given safely to heart transplant pts without an increased incidence of rejection or infection. This information provides clinicians with data to improve clinical practice.