In many instances liver histology remains the "gold standard" for the diagnosis of allograft dysfunction, although progresses in imaging techniques, Doppler blood flow investigation and the availability of serum viral or other markers have somewhat reduced the need for needle biopsy in some situations. Equally, these newly developed techniques have improved our understanding of confounding histological changes. In the early stages after surgery harvesting injury, ischaemia due to interference with arterial blood supply, especially in the young patient, early biliary and/or septic complications have to be distinguished from the classical triad whose relative importance of its 3 components remains incompletely understood. Later in the post transplant course, the differential diagnosis broadens to include late cellular rejection with possible evolution into chronic rejection, late biliary complications, in particular ischaemic cholangitis, de novo or reactivated viral infection, drug toxicity, and potential recurrence of the primary disease, in particular autoimmune disorders and viral hepatitides. Multiple pathologies are not exceptional and should this happens, the putative aetiologies have to be put in order of clinical relevance, especially hepatitis C or B recurrence, and the frequently associated, yet generally mild cellular rejection. Some features such as perivenular cell dropout, chronic hepatitis or architectural anomalies may be difficult to ascribe to a single aetiology. The various pathological changes that may affect liver allografts are selectively reviewed in relation to their likely time of occurrence after transplantation and their use for biopsy interpretation. Areas of controversy are highlighted.