The form of furcation influence both the pathogenesis of periodontal destruction and therapeutic results. The present study was performed to evaluate the effect of root trunk length on clinical outcomes of guided tissue regeneration. Total 30 mandibular first molars were evaluated in this study. Probing pocket depth, clinical attachment level, vertical defect depth and horizontal defect depth were measured at baseline and 6 month after GTR. Correlation coefficients between root trunk length and other clinical measurement were analyzed. The results of this study were as follows 1. The mean root trunk length in lower 1st molar was 2.15 mm. 2. Probing pocket depth, clinical attachment level, vertical defect depth and horizontal defect depth were significantly reduced at 6 month postoperatively compared to values of baseline 3. Correlation coefficient between root trunk length and vertical defect depth at baseline was 0.406 showing the positive correlation 4. Correlation coefficient between root trunk length and horizontal defect depth at baseline was -0.463 showing the negative correlation. 5. Correlation coefficient between root trunk length and decrease of horizontal defect depth after GTR was 0.654 showing the positive correlation. In conclusion, the root trunk length maybe effector for clinical outcome after guided tissue regeneration.