Epidemiological studies associated with breastfeeding have provided conflicting results about whether it is preventive or a risk factor for atopic eczema in children. The current prospective study investigated the relationship between breastfeeding and the risk of atopic eczema in Japan. A birth cohort of 763 infants was followed. The first survey during pregnancy and the second survey between 2 and 9 months postpartum collected information on potential confounding factors and atopic eczema status. Data on breastfeeding and symptoms of atopic eczema were obtained from questionnaires in the third survey from 16 to 24 months postpartum. The following variables were a priori selected as potential confounders: maternal age, maternal and paternal history of asthma, atopic eczema, and allergic rhinitis, indoor domestic pets (cats, dogs, birds, or hamsters), family income, maternal and paternal education, maternal smoking during pregnancy, baby's sex, baby's birth weight, baby's older siblings, household smoking in the same room as the infant, and time of delivery before the third survey. In the third survey, 142 infants (18.6%) were revealed to have developed atopic eczema based on criteria of the International Study of Asthma and Allergies in Childhood. In an overall analysis, neither exclusive nor partial breastfeeding was significantly related to the risk of atopic eczema. After excluding 64 infants identified with suspected atopic eczema in the second survey, both exclusive breastfeeding for 4 months or more and partial breastfeeding for 6 months or more were independently associated with an increased risk of atopic eczema only among infants with no parental history of allergic disorders [multivariate odds ratios were 2.41 (95% confidence interval, 1.10-5.55) and 3.39 (95% confidence interval, 1.20-12.36), respectively]. The authors found that, overall, neither exclusive nor partial breastfeeding had a strong impact on the risk of atopic eczema. However, a parental allergic history may affect the risk.