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Gromwell (LE, Lithospermum erythrorhizon), a perennial herbal plant, has been used for the treatment of various problems associated with atopic dermatitis of the skin, such as water loss, epidermal hyperproliferation, and severe inflammation. Previously, it was shown that oral supplementation with a 70% ethanol extract of gromwell prevented the development of atopic dermatitis in NC/Nga mice. In this study, in order to identify the fraction that mediates gromwell’s efficacy, the dietary effects of water and ethyl acetate fractions from the ethanol extract of gromwell were assessed in the development of dermatitis using NC/Nga mice. Dietary supplementation of the hot water fraction significantly reduced scores for epidermal hyperproliferation in parallel with a marked increase of ceramides. Supplementation of the gromwell hot water fraction also decreased scratching behavior, which was accompanied by a decrease in plasma levels of IgE. These results showed that the hot water fraction of the gromwell ethanolic extract prevented the development of atopic dermatitis by increasing ceramides in NC/Nga mice.