Objectives The aim of this study was to evaluate the effects of Lactobacilli reuteri (Prodentis) alone and in combination with scaling and root planing (SRP) in a double blind, randomized, placebo-controlled clinical trial of volunteers with chronic periodontitis.Methods Thirty, otherwise systemically healthy, chronic periodontitis patients (19 males and 11 females, aged between 34 and 50 years) were included. The study period was 42 days. ‘Split-mouth’ design was used for the SRP, which was performed on day 0; two quadrants (either right or left) were treated with SRP whereas the remaining two quadrants were left untreated. The participants received a toothbrush, toothpaste, and brushing instructions. L. reuteri Prodentis lozenges (1×108 CFU DSM17938+1×108 CFU ATCC PTA 5289) or the corresponding placebo lozenges were taken twice daily from day 21 to day 42. Statistical analysis was done for comparisons of clinical parameters (Plaque Index (PI), Gingival Index (GI), Gingival Bleeding Index (GBI), probing pocket depth (PPD), clinical attachment level (CAL)) and microbiological levels of the pathogens Aggregibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Prevotella intermedia (Pi). All p-values less than 0.05 were considered significant. Assessments were made on day 0 before SRP treatment, on day 21 before administration of the lozenges, and on day 42.Results At day 42, the PI, GI, and GBI were significantly reduced by all treatment modalities. When ranked, the amount of PI, GI and GBI reduction by the different treatments was SRP + Prodentis Prodentis SRP + placebo placebo; all differences were statistically significant. For PPD and CAL, the best result was obtained with the SRP+Prodentis treatment. PPD was reduced from 5.08±0.75 to 3.78±0.61 mm (p<0.001) and CAL from 3.93±0.93 to 2.85±0.74 mm (p<0.001). Prodentis, either alone or following SRP, reduced Aa, Pi, and Pg by 1 log10 unit (p<0.01). The SRP+placebo combination did not significantly affect the levels of the pathogens.Conclusion The present randomized controlled trial confirms the plaque inhibition, anti-inflammatory, and antimicrobial effects of L. reuteri Prodentis. L. reuteri Prodentis probiotic can be recommended during non-surgical therapy and the maintenance phase of periodontal treatment. Considering the beneficial effects of probiotics, this therapy could serve as a useful adjunct or alternative to periodontal treatment when SRP might be contraindicated. Further studies are required in this direction.