BACKGROUND: Food allergy in developed countries represents a growing concern as reflected by epidemiological studies, indicating that up to 4% of the overall population is affected. Reduction of symptoms takes place following eviction or processing of some allergens. However, it cannot be predicted which structural changes will be associated with significant effects on the allergenicity. OBJECTIVE: To determine how various treatments of bovine beta-lactoglobulin (BLG) used as a model antigen alters its immunoreactivity and transepithelial transport, and whether this correlates with reduced allergenicity using an in vitro basophil activation assay. METHODS: BLG was subjected to reduction/alkylation, trypsin digestion or exposed to Lactococcus lactis. The remaining immunoreactivity toward IgG raised against native BLG was assessed by ELISA. Transepithelial transport of BLG and derivatives was examined using polarized Caco-2 cell monolayers mimicking the intestinal epithelium. Selective passage of tryptic peptides was determined using colchicine and cytochalasin D. Basophil activation was measured following stimulation with BLG and derivatives. RESULTS: Reduction/alkylation, trypsin digestion or incubation with L. lactis was associated with decreased BLG recognition by IgG antibodies raised against the native protein. All treatments also resulted in a more efficient transepithelial transport of BLG. BLG crossed the Caco-2 monolayer through passage across the cell, whereas tryptic peptides followed both the para- and transcellular routes. With the exception of denaturation by reduction/alkylation, cross-linking of IgE antibodies by BLG derivatives led to lower basophil degranulation. CONCLUSION: In vitro dissection of antigenicity and allergenicity may be a valid and convenient alternative to evaluate the effects of biotechnological processing on dietary proteins. In addition, it can help to define the molecular and cellular mechanisms that will provide improved means of diagnosis and possibly therapy of food-allergic disorders.