Several recent studies have demonstrated a relationship between the composition of the gut microbiota in infancy and subsequent development of allergic disease. Human milk is the major food in infancy and may thus profoundly influence the composition of the gut flora. Oligosaccharides in breast milk survive the passage through the stomach and are utilized by the gut microbiota. As the relationship between breast feeding and childhood allergy is controversial we hypothesized that the composition of oligosaccharides in breast milk might explain the controversy. Nine of the most abundant neutral oligosaccharides in human milk were analysed in colostrum samples from allergic and non-allergic women and related to subsequent development of allergy in their children. The carbohydrate fraction of the colostrum was separated by gel permeation chromatography and neutral oligosaccharides, tri- to hexasaccharides were collected. Neutral oligosaccharides were analysed with high-performance liquid chromatography. There was a large variation in the concentration of neutral oligosaccharides in colostrum, which could not be explained by the allergic status of the women. Allergic children consumed higher amounts of neutral oligosaccharides in total, although not significantly (p = 0.12). When different oligosaccharides were analysed separately, there was no significant difference in consumption between the infants who developed atopic allergy later (n = 9) and infants who did not (n = 11). Thus, the amount of neutral oligosaccharides in colostrum does not directly correlate with maternal allergy, nor with allergy development in children up to 18 months of age. © 2007 The Authors.