This study compared the therapeutic effects of medium cut-off (MCO) and high flux (HF) dialyzers using metabolomics and proteomics. This was a single-center prospective trial of 20 patients receiving maintenance hemodialysis (HD). A consecutive dialyzer membrane was used for 15-week study periods as follows: 1st HF dialyzer, MCO dialyzer, 2nd HF dialyzer, for 5 weeks respectively. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to identify proteins.