The grain processing industry faces challenges and opportunities to produce new ingredients and foods with added value for consumer health. The HEALTHGRAIN project (www.healthgrain.org) aims to improve health and wellness and reduce the risk of metabolic syndrome-related diseases by providing a scientific basis for increasing the intake of protective compounds in whole grains or their fractions. The project studies variation in composition, process-induced changes, and human metabolism of bioactive compounds in the major European bread grains wheat and rye, and aims to reveal physiological mechanisms underlying their role in the prevention of metabolic syndrome and related diseases. The work is carried out in 17 work packages, distributed over five modules, and carried out by 44 organizations from 15 European countries. We here report on progress in the work.