Examine the adjunctive effect of a Lactobacillus reuteri probiotic (ATCC PTA 5289 & DSM 17938) on the re-instrumentation of residual pockets.This randomized, double-blind, placebo controlled study included 39 previously non-surgically treated periodontitis patients. A re-instrumentation was carried out and probiotic or placebo drops were applied once split-mouth according to the study protocol. Patients afterwards received lozenges to use 2x/d for 12 weeks. Probing pocket depth (PPD), recession, bleeding on probing and plaque levels were analysed, next to the microbiological impact.No effects of the probiotic drops could be found. However, after 24 weeks the overall PPD in the probiotic lozenges group (2.64±0.33mm) was significantly lower compared to the control lozenges (2.92±0.42mm). This difference was even more pronounced in moderate (4-6mm) and deep (≥7mm) pockets. In the probiotic lozenges group, there were also significantly more pockets converting from ≥4mm at baseline to ≤3mm at 24 weeks (67±18% versus 54±17%) and less sites in need for surgery (4±4% versus 8±6%). However, the probiotic products did not influence the microbiological counts of the periodontopathogens.The adjunctive consumption of L. reuteri lozenges after re-instrumentation improved the PPD reduction, without an impact on pocket colonization with periodontopathogens.