In addition to supplying essential nutrients, some food proteins can confer additional health benefits beyond nutrition. The presence of bioactive proteins and peptides in different foods is a factor not currently taken into consideration when assessing the dietary quality of food proteins. The range of described physiological benefits attributed to bioactive proteins and peptides is diverse. Multiple factors can potentially impact on the ability of a bioactive peptide or protein to elicit an effect. Although some food proteins act directly in their intact form to elicit their effects, generally it is peptides derived from digestion, hydrolysis or fermentation that are of most interest. The levels of bioactive peptides generated must be sufficient to elicit a response, but should not be so high as to be unsafe, thus causing negative effects. In addition, some peptides cause systemic effects and therefore must be absorbed, again in sufficient amounts to elicit their action. Many studies to date have been carried out in vitro; therefore it is important that further trials are conducted in vivo to assess efficacy, dose response and safety of the peptides, particularly if health related claims are to be made. Therefore, methods must be developed and standardised that enable the measurement of health benefits and also the level of bioactive peptides which are absorbed into the bloodstream. Once standardised, such methods may provide a new perspective and an additional mechanism for analysing protein quality which is currently not encompassed by the use of the protein digestibility-corrected amino acid score (PDCAAS).