Cardiovascular diseases are the leading causes of mortality in hemodialysis patients. Uremia induced hypertriglyceridemia; increased levels of lipoprotein remnants and low high-density lipoprotein are the main features of cardiovascular risk factors. Also, elevated oxidative stress and inflammation are the main contributors of endothelial dysfunction. Even statin based interventional trials failed to improve mortality in dialysis patients, and different treatment options have been proved to be useful. We aimed to evaluate the effect of dialyzer type on uremia-associated dyslipidemia and endothelial dysfunction. In total 312 patients were enrolled. The initial and 6th month blood samples were obtained from the non-arteriovenous fistula arm on the day before the first hemodialysis session of the week. Flow mediated dilatation of the patients was measured from the same arm before obtaining the blood samples. Patients were on hemodialysis therapy for 76.43 ± 52.7 months. According to their dialyzer type, there has been a statistically significant improvement noted in terms of total cholesterol, low-density lipoprotein-cholesterol, high-density lipoprotein-cholesterol and triglyceride levels. The flow mediated dilatation of the patients are measured as 4.3 ± 0.5 and 4.4 ± 0.4 in baseline measurements of the low flux and high flux groups, respectively. Sixth month values of the patients were measured as 4.34 ± 0.4 and 4.62 ± 0.6. The improvement in low flux groups was not statistically significant but in the high flux group the endothelial dysfunction was significantly improved. Our results show that high-flux dialyzers improved dyslipidemia and endothelial dysfunction in hemodialysis patients. These findings provide a new insight on the selection of high efflux in hemodialysis.