Objective: To determine which biomarkers should be used in a European monitoring system to assess intake of iodine, sodium, iron, folate and vitamin D. These nutrients are relevant for human health but difficult to assess in the diet in a comparable way among countries. Results: Iodine and sodium are mainly excreted in urine. Mean population intakes of iodine and sodium can be estimated by casual urine samples. However, habitual individual intake assessments require multiple 24 h urine collections. Serum ferritin is a sensitive test of iron status (mobilizable storage iron) and continues to be the leading single determination for individual iron status, but with serum transferrin receptor as a promising alternative because it is more specific than ferritin. Erythrocyte folate and homocysteine in blood are markers of folate status which are able to discriminate between normal status and levels of insufficiency in an individual. Serum 25-hydroxyvitamin D is a good marker for vitamin D deficiency in the individual, and can distinguish between overt deficiency and marginal deficiency, especially if combined with serum parathyroid hormone. Conclusions: Specific and sensitive markers for the dietary intake of iodine, sodium, iron, folate and vitamin D are available, which have the advantage of being more accurate than intake estimations derived from dietary surveys. However, the use of biomarkers also has disadvantages such as extra burden in terms of logistics, budget and ethical approval, and can moreover reduce the participation rate. More basic data for the validity of cross-country comparisons are needed and ideas in terms of study design and sampling frame.