Many synthetic polymeric membranes have been widely used for blood purification therapies. Among them polyester polymer alloy (PEPA) membrane shows unique blood compatibility and filtration characteristics.Objective: To evaluate blood compatibility and filtration characteristics of 3 different PEPA membranes, including FLX (PEPA only), FDX (PEPA with polyvinylpyrrolidone, (PVP) as a hydrophilic agent), and FDY (PEPA with PVP) that has larger pore diameter.Methods: Ultrafilters with 3 PEPA membranes (FLX, FDX, FDY, Nikkiso, Tokyo) were compared with those with polysulfone (PS; NK‐PS, Nikkiso, Tokyo) for blood compatibility in vivo. Also, ultrafilters with PEPA, PS, and cellulose triacetate (CTA; FB‐110GA, Nipro, Osaka) membranes were also investigated for filtration characteristics of albumin in aqueous in vitro.Results: FDY, the latest version of the three PEPA, showed excellent small changes in C5a concentration during the treatment right after switching from PS membrane, leaving no significant changes in other biocompatible indices. First 60 min of the time course of s.c. for albumin were shown below taken under aqueous low albumin concentration, i.e., 2.42 × 10−3 kg/dm3. The time‐dependent patterns were totally different from each other in 5 filters. Generally speaking, PS takes a peak value 20–40 min after starting the experiment, depending on the flow conditions. Since PEPA is a hydrophobic material, it showed high s.c. for albumin in FLX (PEPA with no PVP) and never reached plateau. With a hydrophilic agent (PVP), the s.c. greatly reduced in FDX and showed little time‐dependent change. By enlarging the pore diameter in FDY, the s.c. increased in accordance with the enlargement.Conclusion: Newly developed PEPA with PVP has excellent blood compatibility and has unique separation characteristics for albumin.