Summary Background Conflicting evidence exists concerning the protective role of breastfeeding in allergy and atopic disease aetiology. Breast milk contains biologically active molecules influencing the innate immune system of newborns. Objective We aim to assess whether cytokines (TGF-beta1, IL-10 and IL-12) and soluble CD14 (sCD14) in breast milk are influenced by maternal atopic constitution and modify the development of atopic manifestations in infants. Methods Milk samples were collected at 1 month post-partum of 315 lactating mothers participating in the ongoing KOALA Birth Cohort Study. The cytokines and sCD14 were analysed by ELISA in the aqueous fraction. We compared the concentrations of cytokines and sCD14 in breast milk between mothers with and without an allergic history and also with and without allergic sensitization (specific IgE). Associations of cytokines and sCD14 with the development of eczema, wheezing in the first 2 years of life and allergic sensitization of infants at the age of 2 years were analysed by multivariate logistic regression analyses to correct for confounders. Results We found higher sCD14 levels in mothers with a positive vs. negative allergic history (7.6 vs. 7.0 mug/mL; P=0.04) and in mothers who were sensitized vs. non-sensitized (7.8 vs. 7.1 mug/mL; P=0.03). None of the studied immune factors were associated with infant's atopic outcomes. IL-10 was not detected above the detection limit of 0.2 pg/mL. Conclusion Taking together the results of the present and previous studies, we conclude that there is no convincing evidence for a relation between TGF-beta1, sCD14, IL-10 or IL-12 in breast milk and atopic manifestations in infants.