The objective of our studies were seeds of two lupin species Lupinus luteus L. and Lupinus angustifolius L. cvs. Lord and Graf respectively. Lupin seeds were germinated at 15 and 24°C and during two, three and four days. In the lupin sprouts antinutritional factors: alkaloids and raffinose family oligosaccharides (RFOs) and five nitrogen fractions: non protein (Nnp), albumin (A), globulin (G), glutelin and prolamin (Gt+P) and nitrogen residue fraction (Nr) were determined. The level of these compounds was compared with the proper ones of initial material (not germinated seeds). These studies showed that the germination process clearly affects the decrease of antinutritional factors: RFOs and alkaloids. The decrease level of these compounds depended on such factors like, lupin species and used germination conditions. It was found on the base of nitrogen analysis of particular protein fractions that the germination process of lupin seeds causes deep quantitative and qualitative changes in fractional composition of lupin proteins. It especially concerns the decrease of globulin and residual fraction content and distinct increase of Nnp fraction. The changes in other fractions were not so unequivocal in comparison with the mentioned above and depended on lupin species, temperature and time of germination. Qualitative changes of A, G and Gt+P fractions caused by germination were confirmed by gel electrophoresis (SDS-PAGE). The amino acid analysis of seeds and sprouts of Nnp fractions showed an increased content of Asp, Ser, Ala, Pro non essential amino acids (NEAA), and Val, Met, iLeu, Leu, Thr essential amino acids (EAA). Simultaneously a decrease of Glu, Arg (NEAA), Phe, Lis, Cys (EAA) contents was observed. Generally the germination process causes the decrease of total NEAA and an increase of total EAA in Nnp fractions of both lupin species.