Background This study explored the effects of maternal probiotic supplementation on immune markers in cord blood (CB) and breast milk.Methods CB plasma and breast milk samples were collected from a cohort of women who had received daily supplements of either 6 x 10(9) CFU/day Lactobacillus rhamnosus HN001 (n = 34), 9 x 10(9) CFU/day Bifidobacterium lactis HN019 (n = 35) or a placebo (n = 36) beginning 2-5 weeks before delivery and continuing for 6 months in lactating women. CB plasma and breast milk (collected at 3-7 days, 3 months and 6 months postpartum) were assayed for cytokines (IL-13, IFN-gamma, IL-6, TNF-alpha, IL-10, TGF-beta 1) and sCD 14. Breast milk samples were also assayed for total IgA.Results Neonates of mothers who received a probiotic had higher CB IFN-gamma levels (P = 0.026), and a higher proportion had delectable blood IFN-gamma levels, compared with the placebo group (P = 0.034), although levels were undetectable in many infants. While this pattern was evident for both probiotics, when examined separately only the L. rhamnosus HN001 group showed statistically significant higher IFN-gamma levels (P = 0.030) compared with the placebo group. TGF-beta 1 levels were higher in early breast milk (week 1) from the probiotic groups (P = 0.028). This was evident for the B. lactis HN019 group (P = 0.041) with a parallel trend in the L. rhamnosus HN001 group (P = 0.075). Similar patterns were seen for breast milk IgA, which was more readily detected in breast milk from both the B. lactis HN019 (P = 0.008) and the L. rhamnosus HN001 group (P = 0.011). Neonatal plasma sCD 14 levels were lower in the B. lactis HN019 group compared with the placebo group (P = 0.041).Conclusion The findings suggest that supplementation with probiotics in pregnancy has the potential to influence fetal immune parameters as well as immunomodulatory factors in breast milk.