Associations of omega-3 fatty acids (n-3) with allergic diseases are inconsistent, perhaps in part due to genetic variation. We sought to identify and validate genetic variants that modify associations ofn-3 with childhood asthma or atopy in participants in the Vitamin D Antenatal Asthma Reduction Trial (VDAART) and the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC). Dietaryn-3 was derived from food frequency questionnaires and plasman-3 was measured via untargeted mass spectrometry in early childhood and children aged 6 years old. Interactions of genotype withn-3 in association with asthma or atopy at age 6 years were sought for six candidate genes/gene regions and genome-wide. Two SNPs in the region ofDPP10(rs958457 and rs1516311) interacted with plasman-3 at age 3 years in VDAART (p= 0.007 and 0.003, respectively) and with plasman-3 at age 18 months in COPSAC (p= 0.01 and 0.02, respectively) in associationwith atopy. AnotherDPP10region SNP, rs1367180, interacted with dietaryn-3 at age 6 years in VDAART (p= 0.009) and with plasman-3 at age 6 years in COPSAC (p= 0.004) in association with atopy. No replicated interactions were identified for asthma. The effect ofn-3 on reducing childhood allergic disease may differ by individual factors, including genetic variation in theDPP10region.