The present study was undertaken to evaluate the effects of soybean varieties on content of anti-nutritional factors, growth, and nutrient digestibility in rat. For this purpose, the content of trypsin inhibitor and lectin was firstly measured in five soybean varieties. Then sixty male Wistar rats were randomly divided into six groups and fed on different diets as follows: groups 1 to 5 were fed on treatment diets containing five different varieties of soybean flour; group 6 was fed on a control diet containing casein. All animals were fed for four weeks. During this period, faeces and urine were collected to determine the nutritional efficiency of diets and body weight were measured weekly on ten rats from each group. The results showed that trypsin inhibitor and lectin content of Jilin45 was the highest, and those of Jinong7 were the lowest of the soybean varieties. In comparison, all measured parameters, that is including gain in body weight, feed utilization efficiency, nutrient digestibility, nitrogen balance and nitrogen retention, were markedly different among the five groups of animals, but were significantly lower than the control group. These findings show that soybean varieties could significantly affect trypsin inhibitor and lectin content in soybean.