Introduction: Of the most remarkable molecules associated with atherosclerosis and the cardiovascular outcome are S100A12 (10,379.5 Da) and soluble receptor for advanced glycation end products (sRAGE-42,803 Da) in the hemodialysis (HD) population. We designed a study investigating the effects of the medium cut-off (MCO) dialyzers focusing on S100A12 and sRAGE in HD patients compared with low-flux and high-flux dialyzers. Methods: This single-site, prospective, observational study comprises age and sex-matched HD groups (low-flux, high-flux, and MCO). Blood samples were drawn at baseline (predialysis and postdialysis) and the sixth month (predialysis). Results: Groups had similar demographic features and laboratory parameters. Baseline S100A12 levels of the groups were similar [34.3 (±66.5), 30.9 (±42.7), and 40.6 (±29.6); p = 0.13]. Compared to their baseline, the sixth-month S100A12 levels were constant in low-flux and high-flux group and significantly lower in MCO group (p = 0.16, p = 0.33, and p = 0.004). Baseline sRAGE levels of the groups were similar at baseline [2.8 (±0.8), 2.7 (±0.6), and 2.6 (±0.7); p = 0.65], and the sixth-month [2.9 (±0.5), 2.4 (±0.7), and 2.4 (±0.8); p = 0.24]. sRAGE levels remained constant in all groups [p = 0.84, p = 0.13, and p = 0.39]. S100A12/sRAGE ratio at baseline and sixth month was constant in low-flux [22.3 (±63.7) and 18.1 (±24.8); p = 0.17] and high-flux groups [11.9 (±15.3) and 13.1 (±5.8); p = 0.26], the ratio decreased significantly in MCO group [16.5 (±11.6) to 7.8 (±5.5); p = 0.03]. Conclusion: Our study suggests that prolonged use of MCO dialyzers is associated with better S100A12 and sRAGE levels. Long-term studies with larger samples are needed to understand the effects of a better S100A12-sRAGE profile provided by MCO dialyzers on HD patients' cardiovascular outcomes.