Nutritional value of most plant materials is limited by the presence of numerous naturally occurring compounds which interfere with nutrient digestion and absorption. Although processing is employed widely in removal of these factors, selection of cultivars of soya beans with inherently low levels would have a considerable impact on efficiency of non-ruminant livestock production. The review considers the role of plant breeding in achieving this objective. The most abundant trypsin inhibitors are the Kunitz and the Bowman–Birk inhibitors, containing 181 and 71 amino acids respectively. The Kunitz inhibitor is present at a concentration of 1·4 g/kg of total seed contents and the Bowman–Birk inhibitor 1·6 g/kg. A large number of isoforms of the Bowman–Birk inhibitor have been described in soya bean cultivars and it has been shown that the general properties of the inhibitor are, in fact, attributable to different isoforms. Nulls for both Bowman–Birk and Kunitz trypsin inhibitors have been identified, allowing new low trypsin inhibitor cultivars to be produced. However, research into breeding for low trypsin inhibitor cultivars currently has limited application as trypsin inhibitors contribute a major proportion of the methionine content of soya beans. Trypsin inhibitors are thought to be involved in the regulation of and protection against unwanted proteolysis in plant tissues and also act as a defence mechanism against attack from diseases, insects and animals. Hence, in breeding programmes for low trypsin inhibitor cultivars, alternative protection for growing plants must be considered. Use of soya beans in non-ruminant animal feeds is limited by the flatulence associated with their consumption. The principal causes appear to be the low molecular weight oligosaccharides containing α-galactosidic and β-fructosidic linkages; raffinose and stachyose. Non-ruminants do not have the α-galactosidase enzyme necessary for hydrolysing the α-galactosidic linkages of raffinose and stachyose to yield readily absorbable sugars. Soya beans contain between 6·8 and 17·5 g of phytic acid/kg; a ring form of phosphorus (P) which chelates with proteins and minerals to form phytates not readily digested within the gut of non-ruminants. One approach for over-coming the effects of phytic acid is through synthesis of phytase in the seeds of transgenic plants. Currently, recombinant phytase produced in soya beans is not able to withstand the processing temperatures necessary to inactivate proteinaceous anti-nutritional factors present. Soya bean lectins have the ability to bind with certain carbohydrate molecules (N-acetyl-D-galactosamine and galactose) without altering the covalent structure. Lectins are present in raw soya bean at a concentration of between 10 and 20 g/kg. Purified soya bean agglutinin is easily inactivated by hydrothermal treatment but in complex diets binding with haptenic carbohydrates may confer protection against denaturation. The majority of research into soya bean lectins is carried out using laboratory animals so very limited information is available on their in vivo effects in farm animals. This review is concerned specifically with breeding but there are other means of improving nutritive value, for example processing which may alter protein structure and therefore functionality of proteinaceous anti-nutritional factors present.