The response of mandibular Class II facial furcations to guided tissue regeneration treatment with expanded polytetrafluoroethylene barrier membrane (e-PTFE) or freeze-dried dura mater allograft (FDDMA) barriers was evaluated in 11 pairs of molars in 11 patients. Following initial preparation, full thickness flaps were raised in the area being treated, the bone and furcation defects debrided of granulomatous tissue, and the involved root surfaces mechanically and chemically prepared. By random allocation, e-PTFE or FDDMA barriers were fitted over the furcations, secured in place, and the host flap repositioned or coronally positioned. Postsurgical deplaquing was performed every 10 days leading up to e-PTFE removal at about 6 weeks (the resorbable FDDMA did not require removal). Continuing supportive periodontal therapy was provided until surgical re-entry at one year for documentation and any further necessary treatment. Direct clinical measurements demonstrated essentially similar clinical results with both barrier materials for bone and soft tissue changes (few statistically or clinically significant differences). Exceptions were the amount of horizontal furcation fill and the change in the width of the keratinized gingiva, both of which were better with FDDMA (P less than 0.05). Improvements in open probing attachment levels observed at the time of e-PTFE removal were lost over the intervening months, more so for the vertical than the horizontal component of the furcation lesion. Intrapatient comparisons suggested better horizontal furcation responses with FDDMA. The findings of this study suggest equal clinical results with e-PTFE and FDDMA barriers utilizing the GTR technique. These results in Class II mandibular furcations are less favorable than those reported by others. Barrier techniques to handicap the race between different tissues of the periodontal complex appear to be of some clinical benefit and deserve further evaluation.