The aim of this study was to investigate the impact of oral hygiene, periodontal diseases, and dental caries on all-cause mortality in hemodialysis. This prospective cohort study included 266 patients with end-stage renal disease who were undergoing hemodialysis. Medical interviews, blood biochemical tests, and comprehensive dental examinations including periodontal pocket examination on all teeth and dental plaque accumulation by debris index-simplified (DI-S), were performed. Survival rates were assessed at a 3-year follow-up. Overall, 207 patients were included in the longitudinal analysis, and 38 subjects died during the follow-up period. Cox proportional hazards analysis of the multivariate model demonstrated that the highest tertile of DI-S had a significantly higher risk of all-cause mortality than the lowest two tertiles after adjustment for age, sex, smoking habit, body mass index, diabetes, prior cardiovascular disease, hemodialysis vintage, high sensitivity C-reactive protein, albumin, and number of remaining teeth (hazard ratio, 3.04; 95% confidence interval, 1.50-6.17; p = 0.002). Moreover, the number of decayed teeth significantly increased the hazard ratio to 1.21 (95% confidence interval, 1.06.1.37; p = 0.003). This study suggests that accumulated dental plaque and untreated decay, but not periodontal disease, may be independently associated with all-cause mortality in patients undergoing hemodialysis.