This study aimed to utilize micro-computed tomography (micro-CT) analysis to compare new bone formation in rat calvarial defects using chitosan/fibroin-hydroxyapatite (CFB-HAP) or collagen (Bio-Gide) membranes. Fifty-four (54) rats were studied. A circular bony defect (8 mm diameter) was formed in the centre of the calvaria using a trephine bur. The CFB-HAP membrane was prepared by thermally induced phase separation. In the experimental group (n=18), the CFB-HAP membrane was used to cover the bony defect, and in the control group (n=18), a resorbable collagen membrane (Bio-Gide) was used. In the negative control group (n=18), no membrane was used. In each group, six animals were euthanized at 2, 4 and 8 weeks after surgery. The specimens were then analysed using micro-CT. There were significant differences in bone volume (BV) and bone mineral density (BMD) (P<0.05) between the negative control group and the membrane groups. However, there were no significant differences between the CFB-HAP group and the collagen group. We concluded that the CFB-HAP membrane has significant potential as a guided bone regeneration (GBR) membrane.