Native propolis was defined as propolis powder collected from the continental part of Croatia and prepared according to a patented process that preserves all the propolis natural nutritional and organoleptic qualities. Nine phenolic compounds (out of thirteen tested) in propolis sample were detected by high performance liquid chromatography (HPLC) analysis. Among them chrysin was the most abundant (2478.5 microg/g propolis). Contrary to moderate antioxidant activity of propolis examined in vitro (ferric reduction antioxidant power; FRAP-assay), propolis as a food supplement modulated antioxidant enzymes (AOE) and significantly decreased lipid peroxidation processes (LPO) in plasma, liver, lungs, and brain of mice. The effect was dose- and tissue-dependent. The lower dose (100 mg/kg bw) protected plasma from oxidation, whereas the higher dose (300 mg/kg bw) was pro-oxidative. Hyperoxia (long-term normobaric 100% oxygen) increased LPO in all three organs tested. The highest vulnerability to oxidative stress was observed in lungs where hyperoxia was not associated with augmentation of AOE. Propolis protected lungs from hyperoxia by increased catalase (CAT) activity. This is of special importance for lungs since lungs of adult animals are highly vulnerable to oxidative stress because of their inability to augment AOE activity. Because of its strong antioxidant and scavenging abilities, native propolis might be used as a strong plant-based antioxidant effective not only in physiological conditions but also in cases that require prolonged high concentration of oxygen.