The aim of this work was to evaluate the healing of furcation perforation following treatment with Mineral Trioxide Aggregate (MTA) and BioAggregate by histologic examination. The present study was carried out on a total of 72 premolar teeth from 6 adult mongrel dogs. 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 4 weeks. The teeth were classified according to the observation period into three groups; I (one week), II (one month) and III (3 months) (2 dogs each). Each group was further subdivided into three subgroups according to the treatment protocol. These subgroups included; subgroup a (MTA), subgroup b (BioAggregate) and subgroup c (positive control). Inflammatory cell count, epithelial proliferation and new hard tissue formation were assessed. Statistical analysis of the results was carried out and significance of the parameters was determined in the tests at p<0.05. The statistical analysis revealed that MTA and BioAggregate had a similar biological response on the periodontal tissue. There was no significant difference in inflammatory cell count, epithelial proliferation and new hard tissue formation between MTA and BioAggregate subgroups. In conclusion, both MTA and Bioaggregate show similar biological responses when used as a perforation repair material in dogs. These responses showed improved healing characteristics when compared to the control.