BACKGROUND: Endothelial activation in the donor heart has been described variably after brain death and transplantation. We aimed to characterize the time course of endothelial activation in right ventricle (RV) and left ventricle (LV) during the acute phase of clinical transplantation. METHODS: We studied biopsy specimens from the RVs and the LVs of 40 donor hearts: at initial assessment of the donor, at end-ischemia, and after 10 minutes of reperfusion. We also included follow-up RV biopsy specimens at 1 week, 1 month, and 3 months after surgery. Six of the patients had cystic fibrosis and were domino donors. RESULTS: P-selectin and vascular cell adhesion molecule 1 (VCAM-1), but not E-selectin were up-regulated in brain-dead and in domino donors vs controls. Unused donor hearts (n = 6) had significantly less up-regulation of P-selectin and of VCAM-1. We found no difference between the RV and the LV during surgery, but we did see important time-dependent variations. P-selectin was present in 85% of vessels throughout transplantation and decreased to approximately 60% after transplantation (p < 0.001). We initially detected VCAM-1 in 20% of vessels, which decreased to 5% during storage, then increased to 47% at reperfusion, and gradually decreased thereafter (p < 0.001). E-selectin expression increased progressively from 15% initially to 45% at reperfusion and then decreased after surgery (p = 0.001). Thrombomodulin expression was decreased at baseline, and the decrease was accentuated afterward (p = 0.02). Patients with donor organ failure did not have a specific pattern of endothelial activation. CONCLUSION: Cardiac transplantation is associated with marked endothelial activation, with no difference between the two ventricles. The changes persist in the post-operative period, even in the absence of acute rejection.