Nutrient profiles of foods are increasingly used as the scientific basis of nutritional labeling, health claims, or nutritional education. Nutrient profiling schemes are based on sets of rules, scores, or thresholds applied to the nutritional composition of foods. However, there is a lack of scientific validation of nutritional profiling schemes. To develop a reference method using existing dietary surveys, to define a set of indicator foods that are positively or negatively associated with a "healthy diet." Such indicator foods can be used both for establishing relevant nutrient profiles and for the validation of existing or future nutrient profiling schemes. The proposed validation method is based on food and nutrient intakes of adults participating in national dietary surveys in five EU countries: Belgium (n = 2,507), Denmark (n = 3,151), France (n = 1,474), Ireland (n = 1,379), and Italy (n = 1,513). The characterization of indicator foods is divided in two steps. First, "healthy diets" of individuals are identified in the five national dietary surveys by comparison to the Eurodiet reference intakes. Second, indicator foods associated positively or negatively to the "healthy diets" are determined. With a P-value of 10(-3) for the test of comparison of food intakes between the "most healthy eaters" and the "less healthy eaters," it was possible to identify 294 indicator foods out of 1,669 foods tested in the five countries. In all the countries except Italy, there were more indicator foods positively associated than indicator foods negatively associated with the "healthy diet." The food categories of these indicator foods were in good agreement with Food Based Dietary Guidelines like the USDA dietary guideline for Americans. A new reference method for the validation of profiling schemes was developed based on dietary intake data from using dietary surveys in five European countries. Only a minority of foods consumed in these dietary surveys could be used as indicator foods of healthy or unhealthy diets in order to subsequently test nutritional profiling schemes. Further work is needed to build a list of indicator foods that could be considered as a "gold standard."