Nutrient-rich food (NRF) index scores are dietary quality indices based on nutrient density. We studied the design aspects involved in the development and validation of NRF index scores, using the Dutch consumption data and guidelines as an example. We evaluated fifteen NRF index scores against the Dutch Healthy Diet Index (DHD-index), a measure of adherence to the Dutch dietary guidelines, and against energy density. The study population included 2106 adults from the Dutch National Food Consumption Survey 2007–2010. The index scores were composed of beneficial nutrients (protein, fibre, fatty acids, vitamins, minerals), nutrients to limit (saturated fat, sugar, Na) or a combination. Moreover, the influence of methodological decisions was studied, such as the choice of calculation basis (100 g or 100 kcal (418 kJ)). No large differences existed in the prediction of the DHD-index by the fifteen NRF index scores. The score that best predicted the DHD-index included nine beneficial nutrients and three nutrients to limit on a 100-kcal basis, the NRF9.3 with a model R2 of 0·34. The scores were quite robust with respect to sex, BMI and differences in calculation methods. The NRF index scores were correlated with energy density, but nutrient density better predicted the DHD-index than energy density. Consumption of vegetables, cereals and cereal products, and dairy products contributed most to the individual NRF9.3 scores. In conclusion, many methodological considerations underlie the development and evaluation of nutrient density models. These decisions may depend upon the purpose of the model, but should always be based upon scientific, objective and transparent criteria.