To investigate whether re-aeration after a short-term hypoxic pre-treatment (for 2, 12 or 24 h) induces oxidative stress, the temporal sequence of physiological reactions, including the level of free radicals, hydrogen peroxide production, and changes in antioxidative enzymes, was characterized in roots of hydroponically grown lupine (Lupinus luteus L., cv. Juno) seedlings. By using electron paramagnetic resonance (EPR), we found that the exposure of hypoxically grown roots (hypoxic pre-treatment for 12 and 24 h) to air caused an increase in the level of free radicals. The amount of hydrogen peroxide also tended to increase when hypoxically pre-treated roots were re-aerated, which attests to a higher production of reactive oxygen species. Re-aeration caused a higher activity of superoxide dismutase (SOD, EC 1.15.1.1) and catalase (CAT, EC 1.11.1.6), whereas the activity of peroxidase (POX, EC 1.11.1.7) was only slightly influenced. The roots were less tolerant to longer hypoxic pre-treatments, with a significant decrease in viability, associated with death of root tips immediately after hypoxic stress. Roots exposed to hypoxia for 2 h showed less pronounced responses and their viability was not affected by hypoxic stress and re-aeration. These results indicate that re-aeration following short-term hypoxia imposes a mild oxidative stress. This led us to conclude that re-oxygenation stress per se was not the key factor for cell death in root tips.