SummaryBackgroundEarly‐life immune deviation is suspected in the inception of atopic disease.ObjectiveTo investigate the association between cord blood chemokines and the subsequent development of atopic biomarkers and clinical end‐points during the first 6 years of life.MethodsThe Th1‐associated chemokines CXCL10 and CXCL11 and the Th2‐associated chemokines CCL17 and CCL22 were assessed in cord blood of asymptomatic at‐risk newborn children from the Copenhagen Prospective Study on Asthma in Childhood (COPSAC2000) birth cohort and associated with the longitudinal development of biomarkers and clinical end‐points of asthma, eczema, and allergic rhinitis during the first 6 years of life.ResultsCord blood CCL22 levels were significantly associated to total‐IgE levels measured at four time‐points during the first 6 years of life; overall odds ratio, 1.54 [CI, 1.25–1.89; P < 0.0001]. CXCL10 and CXCL11 were not associated with development of any atopic disorders or biomarkers.Conclusion and Clinical RelevanceHigh cord blood levels of the Th2 related chemokine CCL22 were significantly associated with high total‐ IgE levels during the first 6 years of life, but not with specific sensitization, asthma, eczema or allergic rhinitis. This suggests an inborn skewing of the immune system in healthy newborns developing elevated total‐ IgE later in life.