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Aim: To evaluate effects of probiotic Lactobacillus reuteri (L. reuteri) lozenges as an S/RSD adjunct on site-level changes at molars with deep pockets., Materials and Methods: 447 molar sites with pockets ≥ 5 mm from a previous randomized clinical trial of adjunctive L. reuteri lozenges for 28 days were analyzed. Multilevel mixed-effect models (MLM) were constructed to analyze site-level outcomes "change in CAL" and "pocket closure" (residual PPD < 5 mm) in placebo and probiotic groups at 90 and 180 days. Possible patient-, tooth-, and site-level predictors were analyzed as fixed-effects., Results: Estimated change in CAL in probiotic (90 day: 0.87 mm, 180 day: 0.68 mm) was greater than placebo treated molar sites (90 day: 0.73 mm, 180 day: 0.66 mm) and the relative risk (RR) of pocket closure in the probiotic group (90 day: 1.7, 180 day: 1.6) was higher as compared to placebo. Furcation involvement and BOP at site predicted significantly worse treatment outcomes., Conclusion: As compared to S/RSD with placebo, a 28-day course of adjunctive probiotic L. reuteri lozenges improved CAL change at molar sites with ≥ 5 mm deep pockets and conferred a higher probability of shallow residual pocket depth. Presence of furcation-involvement and bleeding on probing worsened treatment outcomes., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)