Rapeseed protein consists mainly of the seed storage protein cruciferin and napin. Cruciferin and napin have different nutritional values and techno‐functional properties. Shifting the cruciferin/napin ratio towards either more napin or more cruciferin could allow diversified applications. The objective of this study was to investigate the genetic variation of cruciferin and napin in modern winter rapeseed cultivars. Cruciferin and napin contents were analysed by SDS‐PAGE. Genetic variation for both protein fractions was highly significant. Heritabilities were high ranging from 74% for cruciferin to 82% for napin. Napin was positively correlated with glucosinolate (rS = .52**) and seed protein content (rS = .48**). Additional plant material with much larger trait variation was included to develop near‐infrared reflectance spectroscopical calibrations. The Near‐infrared reflectance spectroscopy (NIRS) equations showed high fractions of explained variance in cross and independent validation of around .9 for all traits, indicating that the NIRS equations can be applied in routine screening of plant material.