The inducible co-stimulatory molecule, ICOS, is an important regulator of T cell differentiation and effector function. Previously, it was reported that two variants in the ICOS promotor region, g.1-1413G>A and g.1-693G>A, were associated with sensitization to airborne allergens, elevated serum IgE levels and Th2 cytokine production in a Hutterite population. The aim of this study was to evaluate these two and four other selected ICOS variants for association with atopic phenotypes in two large European prospective pediatric cohorts. We investigated subjects from the German Multicenter Allergy Study (MAS), which followed over 800 children with atopic family history from birth until 13 yr of age, and from the Early Treatment of the Allergic Child Study (ETAC), which collected DNA and clinical data of over 330 children with atopic dermatitis during their first 2 yr of life. We genotyped DNA from these children by melting curve analysis using fluorescence resonance energy transfer (FRET) probes. We could not confirm the previously reported association of g.1-1413G>A and g.1-693G>A with atopic phenotypes in our pediatric cohorts. Also four other ICOS variants at putative binding sites for transcription factors showed no association with atopic dermatitis, asthma, allergic sensitization and allergic rhinitis. Our data suggest that these ICOS variants do not play a major role in the development of atopy in European children.