Rapid, cheap, non-destructive, chemical free, accurate and reproducible methods are important tools in the selection for ingredients of crops. In case of yellow endosperm pigments the determination of carotenoids and other compounds by HPLC is both time consuming and expensive. Other method such as spectrophotometry after extraction with butanol is laborious and unpleasant due to the extraction time and odour of the solvent, respectively. Near-infrared spectroscopy (NIRS) is widely applied in different food crops for the determination of a broad variation of ingredients, e.g. protein, carotenoids, fatty acids, oils etc. The objective of the study was to establish a NIRS calibration for yellow endosperm pigments of different wheat species. The results indicated that NIRS discriminated satisfactorily between high and low yellow pigment contents of different wheat genotypes and species. The analysis showed that diploid einkorn wheat was clearly separated from tetraploid and hexaploid species. Moreover, durum varieties were also clearly separated from other tetraploid species/subspecies. It is concluded that NIRS is a valuable selection method to separate a large amount of genotypes in low and high yellow pigment types which subsequently can be analysed by other methods for an exact determination of quantity and quality of endosperm pigments.