There is currently considerable interest in the potential health benefits of isoflavones in functional foods and in the future prospects for the development of new products of benefit to the consumer. The potential health benefits of isoflavones may include protection against age-related diseases including cardiovascular disease, osteoporosis, hormone-dependent cancer and loss of cognitive function. The mechanisms involved may include weak oestrogenic action and antioxidant activity. Our proteomic investigations of changes in the human serum profile in response to the consumption of isoflavones in soya functional foods suggest potentially beneficial modulation of the levels of a number of serum proteins, including increased apolipoprotein E (involved in lipid metabolism) and caeruloplasmin (antioxidant and copper regulatory properties) levels and decreased alpha-1-acid glycoprotein (involved in immunomodulation) levels that may contribute to vascular protection. Furthermore, preliminary metabonomic data indicates an alteration in the urinary metabolite profile after isoflavone consumption, which may be of significance.