Liver transplantation is an effective therapeutic option for end-stage liver disease, but initial poor graft function still occurs, often related to cold preservation–warm reperfusion (CPWR) conditions. Damages to mitochondria could be implicated in hepatocyte cell death since opening of the permeability transition pore (PTP) can lead to necrosis and apoptosis. The purpose of this study was to test the hypothesis that inhibition of mitochondrial permeability transition by cyclosporin A could improve rat liver mitochondrial and hepatocellular parameters after 24-h cold preservation followed by a warm reperfusion in Krebs-Henseleit Buffer. Mitochondrial functions were assessed by measuring respiratory parameters, swelling, cytochrome c release and caspases activation. Hepatocyte injury was assessed by evaluation of ATP energetic charge, lactate dehydrogenase (LDH) leakage, apoptosis and necrosis. Results show that CPWR induces liver mitochondrial and cellular damages. CPWR induced damages on the mitochondrial respiratory chain, leading to mitochondrial swelling. The consequences are the loss of ATP energetic charge, the initiation of apoptosis through cytochrome c release and the activation of caspases. Cyclosporin A partially protects respiratory chain integrity and totally prevents mitochondrial swelling, allowing better recovery of energetic charge. It also partially limits the activation of the apoptotic machinery and subsequent cell death by apoptosis in both the organ and isolated hepatocytes. Inhibition of permeability transition thus provides only partial protection against CPWR. However, this target can be considered as a promising adjunct therapeutic approach to improve the primary function of the grafted liver after transplantation.