By evaluating risks of late mortality and causes of death among long-term survivors after autologous hematopoietic stem cell transplantation (HSCT) in Japan, we clarified what we should focus on during follow-up to reduce them. The study cohort included 6,780 patients who had survived for≥2 years after the first autologous HSCT performed from 1974 to 2012 for hematological diseases. With a median follow-up of 6.0 years among survivors, overall survival probabilities at 5 and 10 years after HSCT were 92% and 83%, respectively. Eight hundred thirty deaths occurred: 451, recurrent primary diseases; 87, subsequent solid cancers; 57, subsequent hematological malignancies; 55, infections; 41, respiratory diseases; 19, cardiovascular diseases; 15, liver diseases; 10, neurological diseases; and 7, kidney/genitourinary diseases(Except small numbers of other causes and missing) . According to the log-rank test, the risk of overall mortality was remarkably increased among HSCT recipients compared with the that in the general Japanese population(observed/expected ratio[O/E] =5.4; 95% confidence interval[CI] , 5.0-5.8) . The risks of cause-specific mortality increased with infection(O/E=6.8; 95% CI, 5.1-8.8) , subsequent solid cancers(O/E=1.4; 95% CI, 1.1-1.7) , subsequent hematological malignancies(O/E=14.3; 95% CI, 10.8-18.5) , kidney/genitourinary diseases(O/E=3.4; 95% CI, 1.4-7.1) , respiratory disease(O/E=9.0; 95% CI, 6.5-1.2) , and liver diseases(O/E=2.6; 95% CI, 1.4-4.2) . Long-term survivors after autologous HSCT are at an increased risk of death due to secondary cancers, infections, and any organ diseases as well as recurrence compared to the general population. When monitoring these patients in the outpatient clinic, it is important for physicians to predict a change in the patient's condition and to start treatment earlier.