Soybean protein is one of the most significant sources of food allergens and intolerance, causing both IgE-mediated allergy and food protein-induced endocolitis syndrome (FPIES). This chapter first discusses the mechanisms causing allergies and infantile food intolerance. It reviews what we know about adverse food responses, the gut’s response to food and the individual soybean proteins that elicit an immunological response. The chapter also discusses how to reduce allergens in soybean plants as well as the particular problem of intolerance in salmonids with implications for aquaculture.