Current research into dietary factors contributing to the development of allergic diseases is directed towards new active approaches instead of passive elimination diets. The present study aimed to investigate the explanatory role of the diet in a probiotic intervention study on the appearance of atopic eczema (AE) in childhood and the safety of perinatal supplementation with probiotics (Lactobacillus rhamnosus strain GG; ATCC 53 103). A prospective follow-up study from birth to 48 months of children (n 159) with a family history of allergic disease was carried out. Outcome measures included growth, dietary intake assessed with 4 d food diaries and their association with AE by logistic regression models. Increased intakes of retinol, Ca and Zn, with perinatal administration of probiotics, reduced the risk of AE, whilst an increase in intake of ascorbic acid increased the likelihood of AE. Perinatal administration of probiotics was safe, as it did not influence the height (mean difference 0·04 (95 % CI −0·33, 0·40) sd scores, P=0·852) or the weight-for-height (mean difference −3·35 (95 % CI −7·07, 0·37)%, P=0·077) of the children at 48 months with and without perinatal administration of probiotics. Up to 48 months, AE did not affect height (mean difference −0·05 (95 % CI −0·42, 0·33) sd scores, P=0·815), but mean weight-for-height in children with AE was −5·1 % (95 % CI −8·9, −1·2 %) lower compared with children without (P=0·010). The joint effects of nutrients and probiotics need to be considered in active prevention and management schemes for allergic diseases.