Soybean is widely utilized in the food and feed industries. However, soybean contains many anti-nutritional factors that limit its extended application. The two most important antigenic proteins are glycinin and β-conglycinin. When young animals are fed diets containing soybean protein, a small portion of undigested proteins enters the lymph and blood through gaps between the intestinal epithelial cells. These macromolecules have considerable antigenic activity and stimulate the immune system resulting in specific antigen-antibody reactions and T lymphoid cell-mediated delayed hypersensitivity. A current focus of research is to develop methods to decrease the immuno-reactivity of soybean proteins. Several strategies have been developed to prevent food allergies including those feed processing and plant breeding. The latest studies indicate that certain kinds of immuno-modulators, such as vitamin C and lipoic acid, may specifically block the IgE mediated anaphylaxis and these may provide new insight into the effective prevention of soybean-induced allergy and perhaps other food allergies. This review is divided into seven parts including (1) Allergenic proteins found in soybean; (2) Structure-function relationships of allergenic proteins in soybean; (3) Extraction, purification and detection of allergenic proteins in soybean; (4) Anaphylaxis induced by allergenic proteins in soybean; (5) The potential mechanism of soybean allergy; (6) Prevention and treatment of soybean allergy; (7) The effects of plant breeding on the antigenicity of allergen proteins in soybean. Being fully aware of the soy protein antigen and finding the methods to eliminate anaphylaxis induced by soybean proteins will help to significantly improve efficiency of soybean protein utilization.