Background: Little information is available regarding the type of dialyzer which results in good prognosis. This study is aimed at investigating the association between 7 types of dialyzers and 2-year mortality. Methods: We conducted a cohort study using data from a nationwide registry of the Japanese Society for Dialysis Therapy. Subjects were 136,676 patients on maintenance hemodialysis (HD) between 2009 and 2011 who underwent maintenance HD for at least 2 years and were treated with one of the following 7 types of high-performance membrane dialyzers: cellulose triacetate (CTA), ethylene vinyl alcohol (EVAL), polyacrylonitrile (PAN), polyester polymer alloy (PEPA), polyethersulfone (PES), polymethylmethacrylate (PMMA), and polysulfone (PS). Cox regression was used to estimate the association between baseline dialyzers and all-cause 2-year mortality, adjusting for potential confounders. Results: Data were adjusted using basic factors, with PS as a reference group, and the hazard ratio (HR) was significantly higher in CTA, PMMA, PAN, and EVAL groups. Further data adjustment for Kt/V yielded the same results as were obtained from data adjusted for basic factors. After further adjustment for nutrition- and inflammation-related factors, HR was significantly lowered for the PES and PMMA groups compared with the PS group (HR 0.88; 95% CI 0.82-0.94 and HR 0.84 95% CI 0.76-0.93, respectively). After propensity score matching, HR for the PES and PMMA groups was significantly lowered compared with the PS group. Conclusions: The use of different membrane types may affect mortality. Further long-term prospective studies are needed to clarify whether the PES and PMMA membranes can improve prognosis.