BACKGROUND: Heating destroys many conformational epitopes and reduces allergenicity of some foods. IgE-epitope binding has been shown to be different among patients who outgrew their cow's milk or hen's egg allergy and those who did not. A significant proportion of milk- or egg-allergic children are tolerant to these foods in their baked forms. We sought to explore the effects of heating on milk and egg proteins and to evaluate for differences in immunolabeling among children with regard to reactivity to heated milk or egg. METHODS: Sera from participants in clinical dietary intervention trials were utilized. Milk and egg samples were variably heated and prepared (at times within a wheat matrix). Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), protein transfer, and Western blot were completed. RESULTS: Sera from 20 milk-allergic and 24 egg-allergic children were utilized. Gel electrophoresis showed strongly staining casein bands that persisted for up to 60 min of heating. In contrast, β-lactoglobulin and α-lactalbumin bands became progressively weaker with increasing heating times, with no detectable β-lactoglobulin after 15-20 min of heating. The ovalbumin band became progressively weaker, whereas ovomucoid remained stable after 25 min of heating. Immunolabeling revealed that all heated milk-reactive children possessed IgE antibodies that bound the casein fraction regardless of heating time. Presence of wheat during heating resulted in decreased IgE antibody binding to milk and egg white proteins. CONCLUSION: Heating has a different effect on whey and caseins in cow's milk and ovalbumin and ovomucoid in hen's egg white. The effect of heat on protein allergenicity is affected by the temperature and duration, along with the presence of wheat.