The number of hematopoietic stem cell transplantations and recipients with late complications from transplantation are both increasing; therefore, we investigated the status of the long-term follow-up system for hematopoietic stem cell transplantation survivors in Japan using a mail questionnaire; 100 of 194 institutions replied. The median examination time for each patient was 12.5 min. Five percent of institutions had an outpatient transplantation clinic, 1% had a manual for long-term follow-up after stem cell transplantation, and 11% used NIH criteria for the diagnosis of chronic GVHD. The lack of human resources, such as doctors, nurses, and other co-medical staff for transplant patients, was a structural problem. In addition, the development of guidelines for Japanese patients and staff education are also required in the clinical process. Thus, a long-term follow-up system, training of human resources, and appropriate reallocation of funds for medical services are required.