We prospectively investigated whether organic food consumption by infants was associated with developing atopic manifestations in the first 2 years of life. The KOALA Birth Cohort Study in the Netherlands (n 2764) measured organic food consumption, eczema and wheeze in infants until age 2 years using repeated questionnaires. Diet was defined as conventional ( < 50 % organic), moderately organic (50–90 % organic) and strictly organic (>90 % organic). Venous blood samples taken from 815 infants at 2 years of age were analysed for total and specific IgE. Multivariate logistic regression models were fitted to control for potential confounding factors. Eczema was present in 32 % of infants, recurrent wheeze in 11 % and prolonged wheezing in 5 %. At 2 years of age, 27 % of children were sensitised against at least one allergen. Of all the children, 10 % had consumed a moderately organic diet and 6 % a strictly organic diet. Consumption of organic dairy products was associated with lower eczema risk (OR 0·64 (95 % CI 0·44, 0·93)), but there was no association of organic meat, fruit, vegetables or eggs, or the proportion of organic products within the total diet with the development of eczema, wheeze or atopic sensitisation. Further studies to substantiate these results are warranted.