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Infants may be sensitized to dietary antigens even during exclusive breast-feeding. Because food antigen traces in breast milk may have harmful effects on gut barrier function in infants with atopy, the authors sought to evaluate whether or not it is beneficial to shift such infants from breast milk to a hypoallergenic formula.Fifty-six infants (mean age, 5.0 months) manifesting atopic eczema during exclusive breast-feeding were studied at weaning to a tolerated hypoallergenic formula. The urinary recovery ratios of orally administered lactulose and mannitol, fecal α-1 antitrypsin and urinary methylhistamine, and eosinophil protein X concentrations were assessed during breast-feeding and after weaning.The median (interquartile range, IQR) concentration of fecal α-1 antitrypsin was 2.3 mg/g (range, 1.2–3.3 mg/g) during breast-feeding and 0 (0.0–1.9 mg/g) after weaning to a tolerated hypoallergenic formula, z = −4.23, P < 0.0001. The urinary recovery ratio of lactulose and mannitol decreased from 0.029 (range, 0.021–0.042) to 0.023 (range, 0.016–0.031), respectively, z = −3.45, P = 0.0006. Concomitantly, the atopic eczema improved, and the concentration of urinary eosinophil protein X decreased significantly.In breast-fed infants with atopy, gut barrier function is improved after cessation of breast-feeding and starting of hypoallergenic formula feeding.