Food antigens transferred into breast milk sometimes cause an allergic reaction in exclusively breast-fed infants. This study will show whether the intake of a whey hydrolysate formula for lactating women (MOM HA) can reduce the appearance of food antigens in breast milk. Lactating women in the MOM group (n = 12) consumed MOM HA as a substitute for cow's milk and those in the COW group (n = 13) consumed cow's milk for more than 4 months. After the ingestion of 200 mL of MOM HA and cow's milk by the women in the MOM and COW groups, respectively, the first breast milk samples were obtained and beta-lactoglobulin was measured using enzyme-linked immunosorbent assay. The number of subjects with detectable beta-lactoglobulin (> 0.1 ng/mL) in the MOM group was two (17%), which was significantly less than that in the COW group (11 subjects, 85%, p < 0.01). The level of beta-lactoglobulin was also lower in the MOM group than the COW group (p < 0.01). Subsequently, the women in the MOM group consumed cow's milk and those in the COW group consumed MOM HA for one week; then a second sampling was performed. beta-Lactoglobulin was detected in three (25%) and 8 subjects (62%) in the MOM and COW groups, respectively. The level of beta-lactoglobulin was still lower in the MOM group (p < 0.05). The consumption of whey hydrolysate formula by lactating women over a considerable time reduces the transfer of beta-lactoglobulin into their breast milk, and the low level can be maintained even after inadvertent ingestion of cow's milk.