With the improvements in post-transplant immunosuppression, the incidence of acute cellular rejection and chronic rejection has decreased significantly over the last few years. This has led to alterations in the presentation of rejection with more patients suffering from late acute rejection, which commonly has different histological appearances compared with the early post-transplant period. There is now a shift in interest to the long-term outcome of liver allografts, with recurrent disease being the most common cause of abnormal histology. The combination of long-term immunosuppression and recurrent disease leads to complex and atypical features on biopsy specimens. Other causes of liver graft inflammation include de novo autoimmune disease and 'idiopathic' post-transplant hepatitis. There is gathering evidence that idiopathic hepatitis can have significant consequences in terms of tissue fibrosis and progression to cirrhosis. Future developments in genetic and immune profiling may lead to liver biopsy becoming a predictive tool to identify patients in which immunosuppression can be safely withdrawn.