Background: Previous studies showed that a probiotic-rich diet may improve the plasma lipid profile and lower the risk of cardiovascular disease (CVD). In a randomized controlled study we tested the possibility for regulation of plasma lipid profile using a kefir that contained the antioxidative probiotic strain, Lactobacillus fermentum ME-3 (DSM14241). The trial was performed in clinically healthy adults with borderline-high serum low-density lipoproteincholesterol (LDL-C) and/or high serum triglyceride (TG) levels based on guidelines from the European Cardiology Society and European Atherosclerosis Society. Methods: One hundred sixty four participants meeting the inclusion criteria were included. Participants were randomised to receive 200 ml/day kefir, either with probiotic (PG; n = 71, 58 females, mean age 49.6 ± 6.5 y) or without probiotic (CG; n = 66, 58 females, mean age 49.9 ± 6.1 y). The probiotic contained 4 × 10 7 cfu/ml L. fermentum ME-3 (total 8 × 10 9 cfu/day). At 4 weeks (n = 71 PG and n = 66 CG) and at 8 weeks (n = 43 PG and n = 33 CG), we evaluated anthropologic, blood biochemical indices, and the faecal temporal persistence of the probiotic strain was assessed by real-time PCR. Results: After 4 weeks, the lipid profiles were mostly similar between groups: only the values of oxidised LDL (ox-LDL) and TG were significantly reduced (P < 0.001 and P = 0.005, resp.). After 8 weeks, the PG group exhibited reductions in LDL-C (5 %, P = 0.001), ox-LDL (6 %, P < 0.0002), TG (17 %, P = 0.033). Next, the ratio of LDL-C to HDL-C was decreased only in the PG (P = 0.013) while in the CG it was significantly increased (P = 0.018). After completing the trial the changes in all above listed indices were significantly (P < 0.05) different between the PG and CG groups. In faeces, the prevalence of L. fermentum ME-3 increased after 4 and 8 weeks (both P < 0.001), but the counts, determined with real-time PCR, remained constant. Conclusions: Eight weeks of consuming kefir with the antioxidative probiotic L. fermentum ME-3, reduced serum LDL-C, ox-LDL and TG values in clinically healthy volunteers with borderline-high lipid profile indices. Thus, L. fermentum ME-3 has potential to lower the risk of CVD that is tightly associated with maintenance of plasma lipid profile. This study was registered as current controlled trial http://www.controlled-trials.com/ISRCTN49744186 as ISRCTN49744186.