Evaluation of survival of teeth with class III furcation involvement (FI) ≥5 years after active periodontal treatment (APT) and identification of prognostic factors. All charts of patients who completed APT at the Department of Periodontology of Goethe-University Frankfurt, Germany, beginning October 2004 were screened for teeth with class III FI. APT had to be accomplished for ≥5 years. Charts were analysed for data of class III FI teeth at baseline (T0), at accomplishment of APT (T1), and at the last supportive periodontal care (T2). Baseline radiographic bone loss (RBL) and treatment were assessed. One-hundred and sixty patients (age: 54.4 ± 9.8 years; 82 females; 39 active smokers; 9 diabetics, 85 stage III, 75 stage IV, 59 grade B, 101 grade C) presented 265 teeth with class III FI. Ninety-eight teeth (37%) were lost during 110, 78/137 (median, lower/upper quartile) months. Logistic mixed-model regression and mixed Cox proportional hazard model associated adjunctive systemic antibiotics with fewer tooth loss (26% vs. 42%; p = .019/.004) and RBL (p = .014/.024) and mean probing pocket depth (PPD) at T1 (p < .001) with more tooth loss. Subgingival instrumentation with adjunctive systemic antibiotics favours retention of class III furcation-involved teeth. Baseline RBL and PPD at T1 deteriorate long-term prognosis.