Objective: To evaluate the tooth loss status of mandibular molars with furcation involvements after 5-year non-surgical periodontal treatment,and to analyze the factors that affected the tooth loss. Methods: A retrospective analysis was conducted in 79 patients with chronic periodontitis, who had received non-surgical periodontal treatment and 5 years of periodontal maintenance treatment in Department of Periodontology, Peking University School and Hospital of Stomatology from 1988 to 2012. Their clinical indexes, including probing depth (PD), bleeding index (BI), furcation index (FI) and tooth mobility were both evaluated before treatment and at the last time of the maintenance treatment. Bone resorption at furcation area was measured at the first visit by periapical radiographs taken by professional doctors of medical imaging. The status of tooth loss after 5-year non-surgical periodontal treatment on mandibular molars with furcation involvement, and the factors that affected the tooth loss were analyzed. Results: (1) Non-surgical treatment was significantly effective on the changes of PD in the patients of chronic periodontitis with furcation involvement, while the presence of furcation involvement could affect the improvement of PD here. (2) PD at the furcation area, tooth mobility, vertical bone resorption, and bone resorption area were all significant risk factors of mandibular molar missing (P<0.001), and the same with FI=3 and FI=4 (P=0.017, P=0.007),while age (P=0.703), gender (P=0.243) and smoking history (P=0.895) were not related to the tooth loss in this study. (3) The risk of tooth loss in mandibular molars with FI≥3 were significantly higher than those with FI≤2, and the survival rate of the former was less than 50%. Conclusion: The loss of mandibular molars with furcation involvement was related to the furcation involvement, meanwhile the degree of furcation involvement and bone resorption can significantly increase the risk of tooth loss.