<i>Background:</i> In previous studies, the major peanut allergen Ara h 1 was digested in vitro using pepsin and porcine gastric fluid. The results suggested that in vivo gastric digestion of allergen protein can be modeled accurately by peptic hydrolysis in vitro. In the current investigation, studies were designed to follow the gastrointestinal (GI) digestion of peanut allergens under true physiological conditions. In vitro digestion with porcine gastric fluid was compared with actual physiological digestion of peanut allergens in the porcine digestive tract in vivo. <i>Methods:</i> Analysis of physiologic digestion was performed in piglets administered a 20-gram bolus of peanut meal followed by periodic sampling and analysis of GI contents. The pH was monitored, and digesta were analyzed by SDS-PAGE and immunoblot analysis. <i>Results:</i> Peanut meal initially neutralized stomach contents to a pH of approximately 7, which was subsequently acidified by HCl secretion within 30 min. Acidification to pH 2–4 resulted in active pepsin digestion of soluble protein in the stomach. Soluble intact protein/allergens were rapidly degraded to pepsin-resistant peptides in the stomach followed by hydrolysis of these fragments in the small intestine. Particulate material was evident in both the stomach and small intestine that could contribute to continued release of peanut allergens Ara h 1, 2 and 3. <i>Conclusions:</i> Porcine gastric digestion of peanut proteins resembles true physiological digestion only under optimal physiologic conditions. Soluble proteins are rapidly digested and insoluble material continues to release IgE-reactive proteins throughout the GI tract. GI digestion of food allergens can play a prominent role when assessing allergens within the context of a food matrix or meal and during the sensitization phase of IgE-mediated allergy.