Beta-lactoglobulin (betaLG) is one of the first foreign antigens encountered by a newborn child, and it is the major allergen causing cow's milk allergy. Heat denaturation causes changes to the protein structure, but the significance of heat-induced changes for immunogenicity or allergenicity is not known. To clarify how heat denaturation affects allergenicity and immunogenicity, we immunized Hooded-Lister rat pups with intra-peritoneal injections of native or heat-denatured betaLG at days 43 and 62 after birth. The animals were then fed native and denatured milk products twice weekly from 73 to 101 days of age with a feeding tube, after which they were allowed cheese and milk ad libitum, until they were killed on day 131. Total immunoglobulin (Ig)E and betaLG-specific IgG1 and IgG2a levels were determined from serum samples. Spontaneous interleukin-4 (IL-4) and interferon-gamma (IFN-gamma) production was measured from duodenal specimens, and specimens of gastrointestinal mucosae were studied for the presence of inflammatory cells. The rats immunized with native betaLG had higher levels of total serum IgE than the unimmunized controls or the rats immunized with heat-denatured betaLG, while heat-denatured betaLG induced a significantly more intensive mononuclear inflammatory cell and eosinophil infiltration in the gastroduodenal mucosa. The betaLG-specific IgG antibody and IL-4 and IFN-gamma responses were similar in the two groups of immunized animals. Hence, denaturation modifies the immunogenic and allergenic properties of betaLG. Heat-denatured betaLG induces a more intensive local reaction in the gastrointestinal mucosa, while there is some evidence for enhanced systemic allergic sensitization by native betaLG.