Background Various indices are applied to evaluate the nutrient (mostly nitrogen, N) use efficiency of plants, but those indices have rarely been compared across different crops, and the co-limitation of growth by nutrients other than N is usually not considered. Aims To conceptually and quantitatively compare the indices of a plant-level, a plant-soil-level and a fieldlevel (difference) method for the assessment of N use across a set of different annual and perennial crops; and to use some plant-level indices for exploring the colimitation of growth by nutrients other than N in wheat. Method Data sets from previously published studies on wheat (grain), maize (feed), potato (starch), grassland ley (feed) and Salix (bio-energy) field-grown in Sweden were re-analyzed. Conclusions This study is first in conceptually and quantitatively comparing various popular N use indices across a wide range of annual and perennial crops; and also proposes a methodology for exploring the colimitation of growth by nutrients other than N. When comparing the plant-level and plant-soil-level methods, the indices relating crop yields to the amounts of plantinternal N were correlated, while the N-uptake indices were not. Only few of the field-level (differencemethod) indices were correlated with indices of the two other methods.