Polish garlic and white and red onions were subjected to blanching, boiling, frying, and microwaving for different periods of time, and then their bioactive compounds (polyphenols, flavonoids, flavanols, anthocyanins, tannins, and ascorbic acid) and antioxidant activities were determined. It was found that blanching and frying and then microwaving of garlic and onions did not decrease significantly the amounts of their bioactive compounds and the level of antioxidant activities ( P > 0.05). The HPLC profiles of free and soluble ester- and glycoside-bound phenolic acids showed that trans-hydroxycinnamic acids (caffeic, p-coumaric, ferulic, and sinapic) were as much as twice higher in garlic than in onions. Quercetin quantity was the highest in red onion among the studied vegetables. The electrophoretic separation of nonreduced garlic and onion proteins after boiling demonstrated their degradation in the range from 50 to 112 kDa.