The antioxidant activity and contents of various polyphenol classes in the seeds of seven soybean varieties of different seed color and one yellow seed cultivar, representing a reference genotype, were evaluated. Total polyphenols and tannins were determined after extraction of plant material with 70% aqueous acetone, and total flavonoids were extracted with methanol and acetic acid, whereas anthocyanins were extracted with 20% aqueous ethanol. In addition, isoflavone content and composition were determined using high-performance liquid chromatography analysis. Antioxidant activity of seed extracts was evaluated by the 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity assay. A positive linear correlation between antioxidant activity and contents of total polyphenols and anthocyanins was established. The highest antioxidant activity was observed in the extracts of black and brown varieties, which also showed high levels of all polyphenol classes examined. Yellow seed had the highest total isoflavone content (3.62 mg/g of dry material). The highest concentration of total daidzein was determined in black seeds (>2.0 mg/g of dry material), and the highest total glycitein and genistein contents occurred in the yellow cultivar (0.53 and 1.49 mg/g of dry material, respectively). According to our results, varieties of black and brown seeds could be of special interest not only for their large content of total polyphenols, ranging from 4.94 to 6.22 mg of gallic acid equivalents/g of dry material, but also for their high content of natural antioxidants such as anthocyanins.