Phenols, along with flavonoids found in soybean seeds [Glycine max (L.) Merr.], are known as active antioxidants and are associated with numerous benefits to the human health, such as prevention of cancer, cardiovascular diseases, osteoporosis and menopausal symptoms. The aim of this study was to evaluate total phenolic content and total flavonoid content of 33 soybean genotypes grown in 2010 and 2011. Analysis of variance showed significant differences between the genotypes and genotype x year interaction for both investigated traits. The total phenolic content in 2010 ranged from 2.330 to 3.227, and in 2011 from 2.121 to 3.164 mg/g of dry weight, expressed as gallic acid equivalents. Flavonoid content in 2010 varied from 0.433 to 0.659, and in 2011 from 0.428 to 0.580 mg/g of dry weight, expressed as catechin equivalents. Genotypes OS-L-100, OS-L-12, and OS-L-17 were singled out for the highest content of total phenols while genotypes OS-L-113, OS-L-17 and OS-L-151 had the highest total flavonoid content on average for both years. Results of analyses presented in this paper contribute to the development of the genetic background for improving antioxidant properties of Croatian soybean varieties.