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 lipoprotein-cholesterol (LDL-C) and/or high serum triglyceride (TG) levels based on guidelines from the European Cardiology Society and European Atherosclerosis Society. 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 × 107 cfu/ml L. fermentum ME-3 (total 8 × 109 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. 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. 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.