Background. Endo-periodontal lesions are bacterial infectious diseases involving both the periodontal and pulp tissues with poor outcomes. It is hard for clinicians to predict their prognosis. The aim of this study is to investigate the factors affecting the prognosis of endo-periodontal lesions. Methods. A total of 140 teeth diagnosed with grade 2-3 endo-periodontal lesions in patients with periodontitis were recruited in this study. They were divided into high and low responder groups, according to the clinical symptoms and parameters of the teeth involved after nonsurgical treatment of both the endodontic and periodontal components. Clinical parameters and symptoms were compared before and after treatment, and gender, age, smoking, and all clinical parameters were compared between high and low responder groups using univariate analyses. Logistic regression was applied to evaluate the independent effects on endo-periodontal lesion prognosis. Results. Compared with the clinical parameters at baseline, the values of tooth mobility (TM), periapical index (PAI), and discomfort when chewing were decreased after endodontic therapy, and the values of periodontal probing depth (PD), clinical attachment level (CAL), sulcus bleeding index (SBI), TM, simplified oral hygiene index (OHI-S), full-mouth periodontitis severity, PAI, and discomfort when chewing were decreased after periodontal therapy. Univariate analysis revealed that smoking, PD, CAL, TM, PAI, clinical crown-root ratio (CR), full-mouth periodontitis severities, and the number of root canals were significantly different between the high and low responder groups (P<0.05). The logistic regression analysis showed that smoking, PD, CAL, full-mouth periodontitis severities, and the number of root canals remained significantly associated with grade 2-3 endo-periodontal lesions in patients with periodontitis (P<0.05). Conclusionsand Practical Implications. High PD and CAL, multirooted teeth, smoking, and serious full-mouth periodontitis indicated a poor prognosis for teeth with grade 2-3 endo-periodontal lesions.