Soybean is grown for its high oil and protein concentration and profile in the seed. Numerous studies have been carried out to determine the underlying genetics of soybean seed composition traits and develop molecular markers that can aid in the breeding of soybean cultivars with enhanced nutritional quality. This chapter considers genetics and breeding of soybean to improve the nutritional value of the seed as the end product. The chapter describes the protein content and profile of soybean seeds before considering breeding soybean for a modified fatty acids profile that could extend soybean oil’s shelf life or address various health or nutritional issues. Finally, the chapter explores how breeding could improve the contents of tocopherols, isoflavones and saponins in soybean seeds, which are known to have important health benefits for humans.