As more patients undergo and survive allogeneic stem cell transplantation more attention is being focused on the study of chronic graft versus host disease. Although the pathophysiology is still controversial, recent advances have been made in our understanding of this disease, including the balance of T helper type 1 and 2 cells, the role of B cells and autoantibodies, graft manipulation and prophylaxis, which may lead to advances in treatment and prevention. The series of recent publications put forward by the National Institutes of Health consensus project on criteria for clinical trials are expected to advance the standards and uniformity of chronic graft versus host disease clinical research.