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Background: The aim of this clinical trial was to evaluate the effect of topically applied povidone-iodine (polyvinylpyrrolidone and iodine [PVP-l]) used as an adjunct to non-surgical therapy of furcation involvements. Methods: Forty-four patients presenting at least one Class II furcation involvement that bled on probing with probing depth (PD) ≥5 mm were recruited. Patients were stratified into two treatment groups: 1) subgingival instrumentation by an ultrasonic device using PVP-I (10%) as the cooling liquid (test); and 2) identical treatment using distilled water as the cooling liquid (control). The following clinical outcomes were evaluated: plaque index, bleeding on probing (BOP), position of the gingival margin, relative attachment level (RAL), PD, and relative horizontal attachment level (RHAL). The N-benzoyl-L-arginine-p-nitroanilide (BAPNA) test was used to analyze the trypsin-like activity in dental biofilm. The clinical and biochemical parameters were evaluated at baseline and 1, 3, and 6 months after therapy. Results: Both groups had similar means of PD reduction and RAL and RHAL gain. At 6 months, these variables were, respectively, 2.31, 1.17, and 1.00 mm in the control group and 2.31, 1.23, and 1.02 mm in the test group. There was also no difference between groups regarding the number of furcation sites presenting RAL gain ≥2 mm. The results of the BAPNA test failed to demonstrate significant differences between groups. Conclusion: Non-surgical therapy can effectively treat Class II furcation involvements, and the use of topically applied PVP-I as an adjunct to subgingival instrumentation does not provide additional benefits. [ABSTRACT FROM AUTHOR]