Objectives: This study aims to compare between the effect of hemihydrated calcium sulphate bone graft granules and biphasic calcium phosphate granules on bone healing of maxillary cystic defects. Patients and methods: Twenty patients (15 males, 5 females; age range, 16 to 40 years with an average of 25 years) with maxillary cystic lesions were included in this prospective, comparative study. Patients were randomized into two groups as group 1 in which the cystic defects were grafted with hemihydrated calcium sulphate bone graft granules (n=10) and group 2 in which the cystic defects were treated with biphasic calcium phosphate granules(SYMBIOS) (n=10). Postoperative assessments were performed for both groups, clinically through detection of any signs of infection, inflammation, or graft rejection; and radiographically. Radiographic assessment was performed by using cone beam computed tomography (CBCT) preoperative and at 6 months postoperatively for measurement of relative bone density and dimensional changes of the cystic cavity. Results: The radiographic results demonstrated a statistical insignificant difference between the medians (IQR) of relative dimension and density changes of cystic defects in both groups after 6 months. Conclusion: Both bone grafts granules have the same effects on bone filling of cystic defects. Also, both grafts are similar in reducing dimensions of cystic cavities during healing.