Objectives: To evaluate the effect of probiotic clinically and microbiologicaly as an adjunctive treatment to scaling and root planing (SRP) in treatment of chronic periodontitis patients. Methods: Thirty, otherwise systemically healthy, chronic periodontitis patients (22 males and 8 females, aged between 30 and 52 years) were included in the study. They were classified into three group, 1st group composed of 10 the patients who received only scaling and root planning, 2nd group were 10 patients who received scaling and root planning in addition of using probiotic L. reuteri Prodentis lozenge from the start of the treatment, 3rd group were 10 patients who received scaling and root planning in addition to probiotic L. reuteri Prodentis lozenge at the third week. The participants received oral hygiene instructions. Clinical parameters (Plaque Index (PI), , Sulcus Bleeding Index (SBI), probing pocket depth (PPD), clinical attachment level (CAL)) and microbiological levels of the pathogens Porphyromonas gingivalis (Pg), and Prevotella intermedia (Pi), were assessed on day 0 before treatment, and at the end of the study after 4 weeks. Results: At day 30, the PI, SBI, PPD and CAL were significantly reduced in all groups. By comparing between groups there was significant difference in clinical parameters between group 2 and group1 also between group 2 and group 3, also the amount of Pg and Pi decrease in all groups but there was no significant difference between the three groups. 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 nonsurgical therapy and the maintenance phase of periodontal treatment. Considering the beneficial effects of probiotics, this therapy could serve as seful adjunct to SRP but further studies are required in this direction.