AIM: To analyze the role of liver biopsies in differential diagnosis after liver transplantation.METHODS: A total of 50 biopsies from 27 patients with liver dysfunction out of 52 liver transplantation cases were included. Biopsies were obtained 0-330 d after operation,in which, 44 were fine needle biopsies, another 6 were wedge biopsies during surgery. All tissues were stained with haemotoxylin-eosin. Histochemical or immunohistochemical stain was done.RESULTS: The rate of acute rejection in detected cases and total transplantation cases was 48.2% and 25.0%,chronic rejection rate in detected cases and total transplantation cases was 14.8% and 7.7%, preservation-reperfusion injury in detected cases and total transplantation cases was 25.9% and 13.5%, hepatic artery thrombosis rate in detected cases and total transplantation cases was 11.1% and 5.8%,intrahepatic biliary injury rate in detected cases and total transplantation cases was 7.4 % and 3.8%, CMV infection rate in detected cases and total transplantation cases was 3.7% and 1.9%, hepatitis B recurrence rate in detected cases and total transplantation cases was 3.7% and 1.9%, the ratio of suspicious drug-induced hepatic injury in detected cases and total transplantation cases was 11.1% and 5.8%.CONCLUSION: Acute rejection and preservation-reperfusion injury are the major factors in early liver dysfunction after liver transplantation. Hepatic artery thrombosis and prolonged cold preservation may result in intrahepatic biliary injury. Acute rejection and viral infection may involve in the pathogenesis of chronic rejection. Since there are no specific lesions in drug-induced hepatic injury, the diagnosis must closely combine clinical history and rule out other possible complications.