Biomarkers have considerable potential in aiding the understanding of the relationship between diet and disease or health. However, to assess the role, relevance and importance of biomarkers on a case by case basis it is essential to understand and prioritise the principal diet and health issues. In the majority of cases, dietary compounds are only weakly biologically active in the short term, have multiple targets and can be both beneficial and deleterious. This poses particular problems in determining the net effect of types of foods on health. In principle, a biomarker should be able to contribute to this debate by allowing the measurement of exposure and by acting as an indicator either of a deleterious or of an enhanced health effect prior to the final outcome. In this review, the examples chosen - cancer (stomach, colon/rectal, breast); coronary heart disease and osteoporosis - reflect three major diet-related disease issues. In each case the onset of the disease has a genetic determinant which may be exacerbated or delayed by diet. Perhaps the most important factor is that in each case the disease, once manifest, is difficult to influence in a positive way by diet alone. This then suggests that the emphasis for biomarker studies should focus on predictive biomarkers which can be used to help in the development of dietary strategies which will minimise the risk and be of greater benefit.