Emerging evidence reveals that the incidence of allergic disorders commencing during childhood is influenced by pre-, peri- and early postnatal environmental challenges. We here highlight biomarkers involved in the purported interaction of a challenged intrauterine environment during pregnancy and the risk for allergies in the children later in life. We propose that the identification of biomarkers during pregnancy may allow early detection of children prone to develop allergies and possibly other chronic immune diseases. Subsequently, therapeutic interventions designed to prevent negative consequences of prenatal environmental challenges on children's immune system would be within reach.