Currently more than 5,000 hematopoietic cell transplantations are performed annually in Japan. Advances in transplantation technology have reduced early transplant-related mortality, and management of late effects after transplantation has become increasingly important for growing numbers of long-term survivors. Late effects include many complications such as chronic graft-versus-host disease (GVHD), recurrent malignancy, secondary malignancies, infection, lung diseases, endocrine diseases, cardiac diseases, chronic renal diseases, iron overload, bone diseases, and psychosocial distress. The leading causes of late mortality were recurrent malignancy, lung diseases, infection, secondary malignancies and chronic GVHD. International and domestic guidelines of preventive practices and management for long-term survivors have been published. Recent study results highlight the need for education of both patients and medical providers about late effects after transplantation, and demonstrate importance of dedicated long-term follow-up program for improving adherence to health care and long-term survival. This review focuses on evidences of long-term follow-up program, and diagnosis and treatment of chronic GVHD based on the 2014 National Institutes of Health criteria.