Previous studies suggest that nutrition during the fetal and neonatal periods may program susceptibility in the offspring to later development of chronic diseases, such as obesity, hypertension, CVD and diabetes. We investigated the effect of the early life consumption of soy protein and genistein on gene expression involved in metabolic syndrome phenotype. SD rats were fed a casein diet (CAS: 200 g casein/kg diet), a soy protein diet (SPI: 200 g soy protein isolate/kg), or a casein + genistein diet (GEN: 200g casein + 250 mg genistein/kg) throughout 2 week before pregnancy, pregnancy and lactation. There was no significant difference in the weights of the dams among groups throughout study periods. Male offspring were studied at 21 d after birth. The male SPI offspring had significantly lower body weight and body fat than the other groups. Serum total cholesterol concentration was significantly lower in the SPI group. The fasting serum glucose and insulin concentrations were not different among groups. Expressions of 15 genes involved in lipid, fatty acid, steroid metabolism were significantly altered in the SPI group compared to those in CAS group (|fold change| ≥ 2.0) as determined by microarray analysis. Therefore, in the present study, we observed that maternal consumption of soy protein during pre‐pregnancy, pregnancy and lactation affects lipid metabolism in the offspring of rats. This work was supported by a grant from Korea Research Foundation.