Background: Periodontal regeneration using complementary and alternative medicine has gained considerable attention recently. Propolis is a resinous hive product collected by honey bees from exudates and buds of plants and mixed with wax and bee enzymes.Objective: The aim of this study was to evaluate the effect of propolis as bone graft substitute in the management of experimental grade II furcation defects, and to compare its effect to nanobone and to Propolis/nanobone mixture. Material and Methods:Sixteen critical-sized furcation defects on the buccal surface of mandibular third and fourth premolars were surgically created in twelve dogs and divided into three groups. Group I; defects were filled with Propolis, Group II; defects were filled with nanohydroxyapatite graft and Group III; defects were filled with a combination of Propolis/ nanohydroxyapatite graft. Histologically and histomorphometric analysis of newly formed interradicular bone height and percentage were performed after one and three months.Results: After one month; the three experimental groups revealed the features of early periodontal tissues regeneration including cementum, newly formed bone with inserted newly formed PDL fibers. The propolis group showed the highest bone height and bone surface area. After three months; denser bone occupying larger surface area of the furcation defect were noted especially in the propolis group. Conclusion:The addition of nanobone to propolis showed better results than nano bone alone especially at early healing stage. However, it didn't show better results than the use of propolis alone.