Chronic graft-versus-host disease is a serious complication in long-term survivors of allogeneic hematopoietic stem cell transplantation, with several organ systems affected. Chronic graft-versus-host disease is an important cause of morbidity and mortality in allogeneic hematopoietic stem cell transplantation. This article reviews the pathogenesis of chronic graft-versus-host disease. In particularly, the role of B cells in chronic graft-versus-host disease is evaluated, as is evident from several studies which have investigated the presence of antibodies as well as studies which have analyzed B cells as a target for immunotherapy. Thirty autoantibodies and 5 alloantibodies have been identified in chronic graft-versus-host disease patients in 24 studies, and 8 autoantibodies and 5 alloantibodies seemed to be strongly associated with chronic graft-versus-host disease. In addition, various studies have observed significant improvements in chronic graft-versus-host disease using the anti-CD20(+) antibody rituximab. However, it appears to be highly likely that both B cells as well as T cells are of major importance in chronic graft-versus-host disease. Further research is required to clarify the pathogenesis of chronic graft-versus-host disease.