Background Allergy has sharply increased in affluent Western countries in the last 30 years. N-3 long chain polyunsaturated fatty acids (n-3 LCPUFAs) may protect the immune system against development of allergy. Methods We prospectively categorized illnesses by body system in a subset of 91 children from the Kansas City cohort of the DIAMOND (DHA Intake and Measurement of Neural Development) study who had yearly medical records through 4 years of age. As infants, they were fed either a control formula without LCPUFA (n=19) or one of three formulas with LCPUFA from docosahexaenoic acid (DHA) and arachidonic acid (ARA) (n=72). Results Allergic illnesses in the first year were lower in the combined LCPUFA group compared to the control. LCPUFAs significantly delayed time to first allergic illness (p=0.04) and skin allergic illness (p=0.03); and resulted in a trend to reduced wheeze/asthma (p=0.1). If the mother had no allergies, LCPUFAs reduced the risk of any allergic diseases (HR = 0.24, 95% CI = 0.1, 0.56, p=0.0.001) and skin allergic diseases (HR = 0.35, 95% CI = 0.13, 0.93, p=0.04). In contrast, if the mother had allergies, LCPUFAs reduced wheezing/asthma (HR = 0.26, 95% CI = 0.07, 0.9, p = 0.02). Conclusions LCPUFA supplementation during infancy reduced the risk of skin and respiratory allergic diseases in childhood with effects influenced by maternal allergies.