Adverse effect of brain death (BD) on organ quality and function has been proposed. Our aim was to review the mechanisms of adverse effects of BD on donor organ quality and present the current preventive methods. Review of literature resulted in about 60 articles in each of studied organs (liver and kidney). The related articles were analyzed to enable us presenting current data about the role of BD. Acutely, BD results in a temporary autonomic storm. With continuation of BD, Ischemia due to microcirculation disturbances could significantly perturb the function and histological structure of the organs. BD could activate immunogenicity and apoptosis through adhesion molecules, cytokines, and chemokines. Release of MCP-1, IL-1, TNF, and TGF-ß and increased expression of ICAM-1, VCAM-1, and CD45 induce more inflammation after implantation. Apoptosis is another important phenomenon, which has been accused in BD damage. BD can induce graft dysfunction after transplantation. Hemodynamic instability accelerates organ dysfunction and immune activation. Adverse effects of higher immunogenicity and apoptosis in the organ should be addressed carefully. Use of catecholamines (dopamine or noradrenaline) in donor could decrease hypoperfusion damage. Single dose of steroids and soluble P-selectin glycoprotein ligand could minimize the adverse effects of BD.