Objective To observe the effects of hypoxia preconditioning on the mitochondria ultrastructure of hepatocyte during liver transplantation in rats. Methods A modified orthopotic liver autotransplantation model was used to simulate liver transplantatation. Seventy two Sprague-Dawley rats were randomly divided into the following three groups:the normal control (group NC), the autotransplantation group (group AT), and the hypoxia preconditioning group (group HP), with twenty four rats in each group. Group HP were given an 8% oxygen atmosphere for 90 minutes before the operation. At 1, 6, and 24 hours after the operation, the rats were killed and the following tests were conducted: 1. The morphology of mitochondria was observed under transmission electron microscopy (TEM); 2.Mitochondria were quantitatively analyzed by a MiVnt image analysis system. Results Hepatic cells in group AT showed typical injury signs under TEM, the appearance of hepatocytes and mitochondria in group HP were much better than the group AT, and the areas, perimeters and diameters of mitochondria in group HP were much smaller than those in group AT by a significantly amount (EM>P/EM><0.05). Conclusion Changes of mitochondria ultrastructure were the early events in hepatocellular damage, which could be relieved by HP.