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Evaluation of mortality trends in dialysis patients is important for improving their prognoses. The present study aimed to examine temporal trends in deaths (all-cause, cardiovascular, noncardiovascular and the five leading causes) among Japanese dialysis patients.Mortality data were extracted from the Japanese Society of Dialysis Therapy registry. Age-standardized mortality rates were calculated by direct standardization against the 2013 dialysis population. The average annual percentage of change (APC) and the corresponding 95% confidence interval (CI) were computed for trends using joinpoint regression analysis.A total of 469 324 deaths occurred, of which 25.9% were from cardiac failure, 17.5% from infectious disease, 10.2% from cerebrovascular disorders, 8.6% from malignant tumors and 5.6% from cardiac infarction. The joinpoint trend for all-cause mortality decreased significantly, by −3.7% (95% CI −4.2 to −3.2) per year from 1988 through 2000, then decreased more gradually, by −1.4% (95% CI −1.7 to −1.2) per year during 2000–13. The improved mortality rates were mainly due to decreased deaths from cardiovascular disease, with mortality rates due to noncardiovascular disease outnumbering those of cardiovascular disease in the last decade. Among the top five causes of death, cardiac failure has shown a marked decrease in mortality rate. However, the rates due to infectious disease have remained stable during the study period [APC 0.1 (95% CI −0.2–0.3)].Significant progress has been made, particularly with regard to the decrease in age-standardized mortality rates. The risk of cardiovascular death has decreased, while the risk of death from infection has remained unchanged for 25 years.