BACKGROUND Up until now, no predictable periodontal regeneration of Class III furcation defects has been demonstrated after treatment with different available techniques. Recently, a bone graft enriched with a peptide was developed and has shown satisfactory results when applied in intrabony defects. The aim of this study was to compare the use of expanded polytetrafluoroethylene (ePTFE) membrane associated (test group) or not (control group) with anorganic bovine-derived bone matrix (ABM)/synthetic peptide, in the treatment of Class III furcation defects in dogs. METHODS Six mongrel dogs were used in this study, and the second and fourth mandibular lower premolars were extracted. Class III furcation defects were surgically created in the third premolars and filled with impression material. Afterwards, the defects were surgically assessed for debridement and root planing. Teeth were randomly assigned into test and control groups. The membranes were removed after 4 weeks, and the animals were sacrificed 12 weeks later. RESULTS Comparisons between groups by the Wilcoxon signed rank test showed no statistically significant differences in the parameters evaluated. In the control group, a new bone area (NBA) of 41.71%+/-24.07%, connective tissue area (CTA) of 36.34%+/-15.50%, and epithelium tissue area (ETA) of 9.39%+/-5.85% were observed. The new cementum extension (NCE) was 24.16%+/-13.18%. The test group presented an NBA of 31.84%+/-12.58%, CTA of 47.72%+/-11.33%, ETA of 9.17%+/-6.81%, and an NCE of 30.13%+/-16.43%. CONCLUSION There was no statistically significant difference between the two therapies: ePTFE membrane associated with ABM/synthetic peptide flow or ePTFE membrane only.