Objective:To evaluate the healing of furcation perforation following treatment with mineral trioxideaggregate and bioaggregate by using both radiographic and histologic examinations.Material and methods:The present study was carried out on a total of 72 premolar teeth from 6 adult mongreldogs. Under general anesthesia, furcation perforation was carried out by using a round bur# 4. The access cavity of all experimental and positive control teeth was left open for 4weeks. The teeth were classified according to the observation period into three groups; I (oneweek), II (one month) and III (3 months) (2 dogs each). Each group was further subdividedinto four subgroups according to the treatment protocol. These subgroups included; subgroupa (MTA), subgroup b (BioAggregate), subgroup c (positive control) and subgroup d (negativecontrol). Radiographic and histologic evaluations were carried out. The results were statisticallyanalyzed, using ANOVA and chi-square tests.Results:The statistical analysis revealed that MTA and BioAggregate had a similar biological responseon the periodontal tissue. There was no significant difference between subgroups (a) and (b)in all groups (P ≤ 0.05).Conclusion Both MTA and BioAggregate cements are excellent materials for furcationperforation repair.