The Osborne protein fractions of seeds of 17 Lupinus albus cultivars from different regions in Portugal (obtained from plants grown at the same location) were analysed. The objective of this work was to examine the variability in the seed protein fractions of such a L. albus germplasm sample in order to disclose existing genetic relationships and to obtain information useful for a breeding program. Globulins and, interestingly, the fraction extracted with NaOH (“glutelins”) were the major seed protein constituents. The several protein fractions were separated by electrophoresis (reducing SDS polyacrylamide gel electrophoresis) and the patterns examined by multivariate analysis. Bands of “glutelins” together with those of glycosylated polypeptides were found to have the highest discriminating capacity. Lupin populations were grouped according to their clinal geographical distribution from north (small-seeded, higher plant architecture and later flowering type) to south (large-seeded, shorter and early flowering type). It is also possible that polypeptide patterns could reflect microclimatic specificities related with altitude and temperature. In fact, one cultivar from the south but from high altitude was grouped with the north plant types adapted to colder and wetter weather, whereas two cultivars from a warmer north region were grouped with the southern types. The results show, in addition, that a general correlation exists between cultivar early flowering characteristics and higher amounts of both total seed protein and glutelins, and lower glutelin glycosylation. Since high seed protein content and early flowering are important aims of lupin breeding programs, these findings on the seed protein fractions could stimulate and direct future research in lupin improvement.