A nutrigenomic-based biomarker is defined as a set of information consisting mainly of quantitative levels of gene expression and/or proteins and/or metabolites that, when appropriately combined, reflects the health status of a given physiologically relevant process. The identification and validation of robust biomarkers is crucial for assessing the potential effectiveness and benefits of health-promoting food compounds. This is the basis for new and competitive economic and health developments in the food sector as covered by the recently harmonized legislation on the emerging 'health claims made on food' in Europe. For a number of physiological functions affected by food compounds there are no useful biomarkers described and for other functions there is a need for earlier biomarkers. This lack is the main bottleneck for the consolidation and expansion of the health claims-based added values in the food sector.