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Hypoallergenic infant formulas are commonly used for genetically predisposed children and infants diagnosed with cow's milk allergy. This study describes both in vitro and in vivo approaches to assess residual allergenicity of partially hydrolysed infant formulas. Electrophoretic patterns indicated that β-lactoglobulin and other whey proteins were largely degraded. For safety reasons, according to the European commission-guidelines, it is required that the sensitizing capacity of hypoallergenic formulas is tested in an animal model. In contrast to whey sensitization, no elevated levels of whey-specific IgE, anaphylactic reactions or drop in body temperature were observed in sensitized mice exposed to whey hydrolysates. This indicates that the whey hydrolysates lost their putative sensitizing capacity in a mouse model using oral sensitization, which is highly relevant in relation to the human situation. In combination with the lost capacity of hydrolysed infant formulas to cross-link human IgE antibodies on RBL-huFcɛRI in vitro, both the sensitization and the challenge phase of the allergic response were studied. This combination of assays is proposed as a strategy for the screening of new hypoallergenic formulas aimed at preventing sensitization in atopic children and avoiding clinical symptoms in infants suffering from cow's milk allergy.