The objective was to assess the effect of protein hydrolysates of β-conglycinin enriched soybean on fatty acid synthase (FAS) activity and adipogenic response of human adipocytes in vitro. The results showed that genotypic changes in soybean protein subunits produced peptide profiles that led to inhibition of FAS and lipid accumulation in vitro. FAS inhibitory potency (IC 50) of soy protein hydrolysates (SPH) ranged from 50 to 175 μM, while lipid inhibition from 15.6% to 45.9%. Protein hydrolysate C2H from a soybean containing the highest total β-conglycinin (46.9%) showed the most potent inhibitory effect on in vitro adipogenesis (46%) and FAS (IC 50 = 50 μM). C2H was composed of dominant peptides from fragments f(85-112) and f(131-132) of β-conglycinin α subunit. Smaller peptides identified as fragments f(330-342) and f(329-342) of α′ subunit were also found. In conclusion, soybean genotypes enriched in β-conglycinin α and α′ subunits are suitable sources of active peptides that inhibit FAS activity and lipid accumulation. © 2009 Elsevier Ltd. All rights reserved.