In this paper, the biological activity of individual groups of antioxidants is discussed with regard to the prevention of two chronic diseases: cancer and cardiac vascular disease. It is pointed out that the cancer etiology is related to oxidative damages of DNA and to activation of pro-carcinogenic factors by free radicals whereas the cardiac vascular disease is initiated by LDL oxidation. The development of both diseases can be monitored by specific biomarkers that appear useful while estimating the developmental rate of pathogenic changes. For the purpose of appraising biological activity of functional foods, molecular analysis of antioxidative effects is employed. A new science has been established: nutrigenomics, which is the study of the effect of human nutrition on his genome functioning.