Early initiation of dialysis had been considered one of the most important methods for better prognosis of dialysis patients. One of the reasons for this was that long-term as well as short-term prognosis was poor with late initiation of dialysis. In this study, we analyzed the effects of residual renal function and comorbidity on both short- and long-term outcomes of ESRD patients. The subjects of this study were 20 854 patients who started renal replacement therapy (RRT) in 1989 and 1990, when we conducted national surveillance for new ESRD patients. The effects of glomerular filtration rate (GFR) at dialysis start and comorbidity conditions on survival were measured. Mortality hazard ratio (HR) was calculated using a Cox proportional hazard model. Multivariate analysis included pre-dialysis estimated GFR, age, sex, and underlying renal disease. The mean age of the subjects was 57.7 years old. Mean GFR at dialysis initiation was 5.00 mL/min per 1.73 m2 and GFR was significantly higher in patients with diabetes. The median survival time from the start of dialysis was 69 months, excluding subjects who died within 3 months; 1-year survival was 89.7%, while 2-year, 3-year, 5-year, 10-year, and 15-year cumulative survival rates were 79.3%, 71.1%, 57.8%, 37.3%, and 26.1%, respectively. For mortality risks, the higher the GFR at dialysis initiation, the worse the HR for mortality in both short-term and long-term prognoses by unadjusted analysis. However, after adjustments for age, gender, underlying renal diagnosis, and symptom at dialysis initiation, both late and early initiation of RRT did not affect long-term prognosis.