The pathological complications of bone marrow transplantation are complex and may affect any organ in the body. The causes are often multifactorial and include the effects of chemotherapy, the conditioning regimen, drugs used in the post‐transplant period such as immunosuppressants and antibiotics, graft‐versus‐host disease (GvHD) and the effects of the primary disease itself. Infections are common and result from the immunosuppressive effects of cytotoxic drugs and irradiation, GvHD and marrow failure. Haemorrhage is not infrequent. Graft‐versws‐host disease remains a significant problem and can be difficult to diagnose. Some of its histological features simulate the effects of chemo‐radhtion and the diagnostic lesions may not be present early in the disease, when treatment is most effective. Evidence has accumulated that inflammatory cytokines have a key role in the pathogenesis of GvHD. It can be prevented by eliminating T‐cells from the donor marrow but this procedure adversely affects marrow engraftment, increases the chances of rejection and results in a higher incidence of leukaemic relapse. Immunohistochemical staining for various cytokine‐inducible molecules has led to some improvement in early diagnosis.