Introduction: Chronic periodontitis is a slow progressing, multifactorial inflammatory disease of the periodontium that may lead to its destruction, which is detectable as increasing probing pocket depth (PPD), subsequent tooth mobility and tooth loss. The purpose of this systematic review is to update and appraise the current trial evidence to the question do probiotic (L. reuteri) lozenge taken twice daily over 3 to 4 weeks reduce probing pocket depth in patients with chronic periodontitis after 3 months. Methods and analysis: We will conduct reference checks of previous systematic review and trial reports to the topic. PubMed, Scopus, Cochrane library and the Directory of Open Access Journals (DOAJ) will be searched. All selected trial reports will be independently appraised by two reviewers, using the CQS2B trial appraisal tool. Metaanalysis will be conducted using a random effect model with inverse variance method, stratified according to CQS2B corroboration levels (C1 to 4). The I square test with 95% Confidence Interval will be used to establish whether any statistical heterogeneity between datasets exist. Sensitivity analysis will be conducted for metaanalysis results of trials that were rated with onescore at all four CQS2B appraisal criteria, by excluding trials in which: Patients were smokers; Patients were Type II diabetics; Adjunctive antibiotic therapy was provided. For meta-analyses including data of at least four trials, which have been rated with a 1-score for all four appraisal criteria, the results will be further statistically tested for possible selection bias. Publication bias risk will be quantitatively assessed by use of Eggers regression. Ethics and dissemination: Ethical approval is not required for literature-based studies. The results will be disseminated as a prior preprint version and subsequent peer-reviewed publication.