Purpose: The aim of the present pilot study was to investigate the microbial profile in saliva and supragingival plaque samples collected from caries-active adolescents before and after a daily short-term intake of milk supplemented with the probiotic bacteria. Materials and Methods: The present study group consisted of 18 caries-active adolescents of both sexes who volunteered for participation giving an informed consent. The study has a randomised placebo-controlled double-blind pilot design with two parallel arms. After a 2-week run-in period, the subjects were instructed to drink 2.5 dl of milk supplemented with Lactobacillus rhamnosus LB21 (10⁷ CFU/ml) (test) or standard control milk (placebo) once daily for a period of 2 weeks (intervention period). Samples of stimulated whole saliva and supragingival plaque were collected at baseline (after run-in) and immediately after the end of the intervention period (follow-up). The salivary levels of mutans streptococci and lactobacilli were estimated by conventional culturing on selective agar plates. The presence and level of 19 oral species associated with the caries process were determined using the checkerboard DNA-DNA hybridisation technique. Differences between the groups were assessed using the non-parametric Wilcoxon-Mann-Whitney and chi-square tests. Results: The mean caries experience was high with an average of 7.0 ± 3.8 proximal enamel lesions. The most prevalent dominating species in the plaque samples were Streptococcus mitis, Veillonella parvula and Streptococcus gordonii. The saliva samples displayed a more mixed profile, with Streptococcus mitis, Rothia dentocariosa, Lactobacillus casei and Lactobacillus curvata being frequently identified species. All of the subjects harboured mutans streptococci in their saliva, with 61% of them colonised with salivary lactobacilli. No statistically significant differences in the microbial profiles or the estimated counts between the baseline and follow-up samples, or between the two study groups, were observed. Conclusions: The present study showed that a short-term daily intake of milk supplemented with the probiotic bacterium L. rhamnosus LB21 did not significantly affect the microbial profiles or the levels of caries-associated bacteria in saliva and supragingival plaque samples collected from caries-active adolescents. Keywords: adolescents, biofilm, caries, DNA-DNA hybridisation, saliva