High quality traditional whole soybean shoyu, such as Mitoku's Kagisa and Johsen products, accounts for less than one percent of Japan's production. Over ninety-nine percent is commercial soy sauce, which is made using hexane-defatted soy beans, fermented at high temperatures for three to six months and often bottled with additives. An even lower grade product, called synthetic soy sauce, is often sold in supermarkets. This product is not even fermented, but is a mixture of hydrolyzed soy protein, color additives and flavoring agents.

Since shoyu is a fermented soy food, like miso, it shares many of miso's medicinal and nutritional properties while avoiding the problems associated with unfermented soy foods. (See Miso Health Benefits.) Scientists have given particular attention to the high concentration of "brown pigment" in shoyu, because of its strong anti-oxidant and anti-cancer properties. Shoyu is said to aid in the digestion of grains and vegetables while being rich in several minerals. Shoyu is an excellent substitute for salt in all types of cooking.