The effect of soybeans varieties and the extraction ratios on the chemical composition of the resulting soymilk, additionally the effect of the preparation technique of soymilk and soy-yoghurt on the trypsin inhibitors, urease activity and phytic acid contents were investigated. Soybean seed varieties "Clark and Crawford" and their structural components were analyzed for major chemical composition and soluble carbohydrates. Moreover, the changes in the soybean anti-nutritional factors affected by preparation technique of soymilk and soy-yoghurt were determined. Cotyledon of Clark variety contained significantly (p<0.05) lower moisture and total soluble sugars in particularly stachyose compared with that their values of Crawford variety. Soymilk constituents increased with decreasing the amount of water used in the extraction process (1:10 to 1:4 cotyledon: water). Soymilk processing under alkaline conditions showed completely destroyed trypsin inhibitors and urease activity and markedly reduced the amount of phytic acid in soymilk and consequently soy-yoghurt. The results showed that the effectiveness of soybean varieties and the processing technique used in the preparing of soy milk and soy-yoghurt in removing the negative effect of the anti- nutritional factors.