The need for guidance regarding appropriate systematic long-term follow-up (LTFU) of hematopoietic cell transplantation (HCT) survivors has been recognized. Guidelines for screening and preventive practices for HCT survivors were published in 2006. An international group of transplantation experts updated the recommendations in 2011. Several points regarding the management of late complications must be addressed. Therefore, it is difficult to assess them all at routine visits to the hospital. We herein report the LTFU system employed in the Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital. The main purposes include the assessment of chronic GVHD severity, the management of late complications, and patient education for the prevention of infections. We created handbooks for the management of late complications. The questionnaire answered by patients revealed that 93% could understand the necessity for screening of second malignancies and that 84% were satisfied with the LTFU system. The LTFU system is used to provide long-term support according to the patients' social circumstances.