The current review will examine the field of food intake biomarkers and the potential use of such biomarkers. Biomarkers of food intake have the potential to be objective measures of intake thus addressing some of the limitations associated with self-reported dietary assessment methods. They are typically food derived biomarkers present in biological samples and distinct from endogenous metabolites. To date, metabolomic profiling has been successful in identifying several putative food intake biomarkers. With respect to food intake biomarkers there has been a proliferation of publications in this field. However, caution is needed when interpreting these as food intake biomarkers. Many have not been validated thus hampering their use. While much of the focus to date is on discovery of food intake biomarkers there are excellent examples of how to utilise these biomarkers in nutrition research. Applications include but are not limited to: (1) measurement of adherence to diets in intervention studies (2) objectively predicting intake with no reliance on self reported data and (3) calibrating self reported data in large epidemiological studies. Examples of these applications will be covered in this review. While significant progress is achieved to date in the food intake biomarkers field there are a number of key challenges that remain. Examples include lack of databases focused on food derived metabolites thus hindering the discovery of new biomarkers and the need for new statistical approaches to deal with multiple biomarkers for single foods. Addressing these and other key challenges will be key to development of future opportunities.