In a previous study in dogs, the early removal of expanded polytetrafluoroethylene (ePTFE) membrane (2 weeks after placement) showed histomorphometric results (of new bone, cementum and periodontal ligament) similar to that obtained with membrane removal at 4 weeks after placement. This study evaluated the influence of early removal of an ePTFE membrane on the treatment of Class II furcation defects. Twelve patients who provided 12 pairs of mandibular furcation defects were recruited for the study. Baseline clinical measurements were recorded: plaque index (PI), gingival index (GI), bleeding on probing (BOP), probing depth (PD), gingival margin position (GMP) and relative clinical attachment level (RCAL). Full flaps were elevated and hard tissue measurements were performed during the surgery: relative vertical (RVBL) and horizontal (RHBL) bone level. The ePTFE membranes were adapted and sutured to their correspondent tooth and removed at 2 weeks in the test group (TGr) and at 4 weeks in the control group (CGr). After 1 year all sites were re-entered, and soft and hard tissue measurements were recorded. There were no statistically significant differences between TGr and CGr for any baseline measurement. After 12 months, there were no statistically significant differences between TGr and CGr in the PD (p=0.74), GMP (p=0.76) and RCAL (p=0.44) values. However, the RHBL resolution was significant for both groups (CGr p=0.01 and TGr p=0.02), without difference between groups (p=0.39). Early removal of membranes did not affect the outcome on the treatment of Class II furcation defects.