The objective of this study was to investigate the effects of anti-nutritional factors on performance, viscus organ morphogenesis, blood physiological and biochemical parameters and histology of intestine in rats of three different Chinese cultivars raw soybean. Thirty (50±2) d Wister rats were randomly allocated to 3 groups with 10 replicates of 1 rat according to single factor completely randomized design. The three groups rats were fed the diets containing raw soybean cultivars: Jinlinxiaoli 6, Jilin 45 and fengjiao 7607, respectively. The experiment lasted for 30 days. The content of soybean trypsin inhibitor (PI) and soybean agglutinin (SBA) was examined in three different cultivars raw soybean. The results showed that, the content of PI in jilinxiaoli 6 and fengjiao 7607 cultivars raw soybean was significantly higher than that in jilin 45 (P<0.05), and the content of SBA in jilinxiaoli 6 cultivars raw soybean was significantly higher than that in fengjiao 7607 and jilin 45 (P<0.01). Compared with jilin 45 group, the pancreas weight and jejunum villus height (JVH) of rats fed the diets containing jilinxiaoli 6 cultivars raw soybean were more than 22.6% and 39.4% (P<0.05); compared with jilinxiaoli 6 and fengjiao 7607 groups, the jejunum crypt depth (JCD) of rats fed the diets containing jilin 45 cultivars raw soybean was more than 8.8% and 8.4% (P<0.05), respectively. In conclusion, the effects of anti-nutritional factors in feeding rats with raw soybean diets are Jinlinxiaoli 6＞fengjiao 7607＞Jilin 45.［Chinese Journal of Animal Nutrition, 2010，22（3）:734-740］