Flavonoids are a big group of polyphenols of low molecular weight with in vitro antioxidant properties. In this study, the laccase and tyrosinase from Ustilago maydis were partially characterized and their effect on the antioxidant activity of some phenolic compounds was investigated. Since enzymatic polymerization of the phenolic compounds was detected, the size of the aggregates was determined and related to their antioxidant activity. Morphology of the polymers was analyzed by atomic force microscopy. The results showed that the laccase- and tyrosinase-catalyzed polymerization of quercetin produced aggregates with relatively low molecular weight and higher antioxidant activity than the monomeric quercetin. In the case of kaempferol, the aggregates reached higher sizes in the first 2 h of reaction and their antioxidant activity was increased. In the last case, the aggregates adopted fractal-ordered shapes similar to coral in the case of the kaempferol-laccase system and to fern in the case of the kaempferol-tyrosinase system. The kaempferol and quercetin polymers at low concentration had strong scavenging effect on Reactive oxygen species (ROS) and inhibition of lipoperoxidation in human hepatic cell line WRL-68.