Background: To facilitate healing, bone defects are often grafted with bone substitute materials, for example of xenogenic origin or laboratory made alloplasts. An essential process for healing in bone defects is remodeling; thus, long-term use of specific drugs that interfere with bone remodeling may compromise healing of bone defects despite the use of substitute materials. Cyclosporine is an immunosuppressive drug used for the treatment of autoimmune disorders and in the prevention of organ rejection in transplant patients. Pre-clinical studies have shown that use of cyclosporine reduces bone density and also impairs healing of vascularized allografts and dental implant osseointegration. There is limited information on the effect of cyclosporine use on the healing of bone defects grafted with substitute materials. Aim/Hypothesis: To evaluate by means of micro-CT the effect of systemic administration of cyclosporine on the healing of critical- size calvaria defects in rats, grafted with deproteinized bovine bone or biphasic calcium phosphate. Material & Methods: Sixty rats were divided in two equal-sized groups. Animals in one group received systemic administration (per os) of Cyclosporine Csa (10 mg/kg/day) and those in the other group received sterile saline. After 15 days, a cylindrical critical- size defect (5 mm in Ø) was created in the calvaria of the rats. The defects were grafted with a standardized quantity of deproteinized bovine bone (BO group) or biphasic calcium phosphate (b-tricalcium phosphate 40%/hydroxyapatite 60%) (BC group) or were left empty for spontaneous healing (E group), i.e. 10 animals per treatment combination. Use of Cyclosporine or saline was continued for 15 and 60 days post-operative, where five animals per treatment combination were euthanized. Blocks of specimens containing the defect and surrounding tissues were scanned with micro-CT, operated at 50 kV and 800 mA and with image pixel set of 17.48 lm. Transaxial sections – each 35 lm thick – were generated throughout the dataset and 40 equidistant sections comprising the entire defect volume were selected for analysis. A circular region of interest (5 mm in Ø) was superimposed on the defect and the relative quantities of tissues within each defect was estimated semi-automatically by dedicated software using a gray-scale threshold between 55 and 250 to evaluate the percentage of mineralized tissues (new bone and biomaterial; MT), and a threshold of 55 and 90 to evaluate the percentage of bone. Non-paired t-tests and one-way ANOVA/Tukey tests were used to evaluate differences (P < 0.05). Results: Cyclosporine treated animals showed significantly less bone in E defects comparing to animals receiving saline at both experimental periods (15 days: 11.3 3.3 vs. 28.0 3.9; 60 days: 7.6 2.22 vs. 34.8 9.0). Cyclosporine treated animals showed also significantly less MT compering to saline controls in BC grafted defects at 15 days of healing (36.6 6.7 vs. 53. 10.1), but not after 60 after days (46.3 11.1 vs. 42.7 10.6). In BO grafted defects, systemic administration of cyclosporine resulted in reduced amounts of MT comparing to saline controls at 15 days (51.9 9.4 vs. 65.9 14.1; P > 0.05), but not after 60 days of healing (61.7 6.9 vs. 65.2 12.8). At 15 days of healing, the amount of residual bone substitute was significantly less in the cyclosporine group comparing to that observed in the saline group (BO: 32.5 11.5 vs. 50.9 13.8; BC: 17.2 4.5 vs. 32.2 12.2). Conclusion & Clinical implications: Systemic administration of cyclosporine impaired bone healing in critical-size calvaria defects in rats during the early healing period. In addition, systemic administration of cyclosporine accelerated resorption of bone substitute materials during the early healing period.