Background: The kidney has an important effect on minerals and bone metabolism in humans. Kidney is the target organ of many regulating hormones such as parathyroid hormone (PTH) and fibroblast growth factor-23 (FGF-23), also it activates vitamin D. Abnormalities in phosphorus, calcium, vitamin D and parathyroid hormone are common in patients with chronic kidney disease (CKD). Objective: To compare the effect of online hemodiafiltration (HDF) dialysis versus high flux hemodialysis on bone markers. Patients and Methods: The study was performed on 50 prevalent hemodialysis (HD) patients in Ain Shams University Specialized Hospital on high flux dialysis and were divided into 2 groups (group 1), 25 patients who continued hemodialysis with high flux dialyzer and (group 2), 25 patients who were shifted to online HDF. Bone specific alkaline phosphatase (BSAP), calcium, phosphorus, blood urea nitrogen (BUN), creatinine, sodium, potassium and blood hemoglobin were measured at the start of this study and after 4 months. Only Parathyroid hormone (PTH) was measured at the end of the study in both groups. Results: there was significant increase BSAP and significant reduction of phosphorus levels after 4 months with online HDF compared to high flux HD; p value 0.036 and <0.001 respectively. Conclusion: Online HDF has significant effect on bone markers and phosphorus clearance than high flux Hemodialysis but we need more prospective with longer durations studies to confirm this effects.