Soy sauce is a traditional fermented seasoning of East Asian countries and is available throughout the world. In Japanese soy sauce (shoyu), soybeans and wheat are the two main raw materials, used in almost the same quantity. Proteins of the raw materials are completely degraded into peptides and amino acids by microbial proteolytic enzymes after fermentation, and no allergens of the raw materials are present in soy sauce. In contrast, polysaccharides originating from the cell wall of soybeans are resistant to enzymatic hydrolyses. These polysaccharides are present in soy sauce even after fermentation and termed shoyu polysaccharides (SPS). Soy sauce generally contains about 1% (w/v) SPS and SPS exhibit potent antiallergic activities in vitro and in vivo. Furthermore, an oral supplementation of SPS is an effective intervention for patients with allergic rhinitis in two double-blind placebo-controlled clinical studies. In conclusion, soy sauce would be a potentially promising seasoning for the treatment of allergic diseases through food because of its hypoallergenicity and antiallergic activity.