Effects of soaking and cooking methods on physicochemical characteristics, nutrients and antinutrients in twenty soybean genotypes were studied. Batches of seeds were soaked for 18 h in distilled water, 1% citric acid and 2% sodium bicarbonate solutions at room temperature and then boiled in water. Raw soybean genotypes exhibited 36.5-43.2% protein, 20.7-22.2% oil, 2.5-8.3% total soluble sugars, 1.1-10.4% sucrose, 11.1-18.8 mg/g tannins, 14-36.2 mg/g phenols, 5.1-24.5 mg/g phytate, 30-102.5 mg/g trypsin inhibitor activity and 9.3-27 mg/g saponins. Soaking in distilled water and/or different solutions followed by cooking resulted in significant reductions in the levels of protein, oil and antinutrients and enhanced the carbohydrates in soybean seeds. Cooking of soaked seeds resulted in higher losses of antinutrients in comparison to unsoaked seeds. Among the various treatments, soaking in 1% citric acid solution followed by cooking for 30 min resulted in maximum reduction in most of the antinutrients studied.