Production of soybeans and consumption of soy products is increasing worldwide mainly due to acclaimed health benefits. Processing can alter soybean sensory appeal, nutritive value and potentially affect consumer health. This review of the literature examines these issues. Despite potential changes in nutritive value during processing, soy foods processing below 100 o C for short periods, may not adversely affect nutritive value. However, heat inactivation of trypsin inhibitors, denaturation of soybean globulins and haemagglutenins, increases soy protein bioavailability. Excessive heating can impair nutritive value by making lysine unavailable, as serine, cystine and cysteine are converted to a dehydroprotein intermediate that reacts with lysine to form lysinoalanine. Tryptophan and methionine are also lost during excessive heating. The acylation reaction catalyzed by alkali, generates lysinoalanine, an unavailable and potentially toxic compound. In rats, ingestion of lysinoalanine results in diarrhoea, pancreatic hyperplasia, and loss of hair. At levels present in foods, protein-bound lysinoalanine does not cause nephrotoxicity in humans. Heat treatments at alkaline pH result in destruction of arginine, which is converted to ornithine, urea, citrulline and ammonia, while cysteine is converted into dehydroalanine. Serine, threonine and lysine are also reduced at alkaline pH. These conditions may be present during alkali refining of soy oil. Carbohydrates with free reducing groups react with carbonyl groups on proteins as part of the Maillard reaction. Heat treatments at alkaline pH and above 200 o C cause isomerization of amino acids, leading to formation of racemic mixtures of L and D forms. Since D isomers have reduced bioavailability and some including D-proline are reported to be toxic, racemization of an essential amino acid reduces its nutritional value. Changes in lipids include oxidation, loss of lipid-soluble vitamins and change of fatty acids from cis to trans isomers. Autoxidation of unsaturated fatty acids initiates free radical formation leading to destruction of unsaturated fatty acids, with potential reduction of essential fatty acid content. Oxidized lipid-protein interaction products are important precursors of atherosclerotic plaques in vivo. Carotenoids are lost on bleaching, thereby reducing Vitamin A potential. Vitamin E is lost during oil refining. Roasting and toasting have no effect on soy isoflavones, but organic solvents remove them, while fermentation increases their bioavailability. Dehulling reduces total mineral content but most soy minerals follow protein or meal, while sodium and potassium are lost in wash water. To minimize adverse changes, minimal washing, fermentation, reduction of hydrogenation temperature and thermal processing below 100 o C for short periods, are recommended.