Black soybeans were germinated with or without Rhizopus oligosporus for 3 days. The samples collected from each day were freeze-dried and extracted with chloroform-methanol-water mixture to simultaneously obtain organic phase (lipophilic extract) and aqueous phase (hydrophilic extract). In the lipophilic extract, α-, γ-, and δ-tocopherol were drastically decreased by 51%, 97%, and 88%, respectively, after 3 day germination under stress. On the other hand, the lipid peroxide concentration was increased in the fungi stressed, germinating beans from day 2 onward, while it was continually decreased in the nonstressed germinating counterpart. The change of antioxidant capacity (ORACoil value) was correlated to the changes of tocopherols and lipid peroxide concentrations. In nonstressed germinatng beans, ORACoil value dropped by 38% after 3 days, while in the fungi-stressed germinating beans, ORACoil was decreased by 80%. In hydrophilic extract, the antioxidant activity, measured by ORAChydro assay, is about 80 times higher than the ORACoil values, but there is no significant change before and after germination (either with or without stress). The total phenolic content in the hydrophilic extract increased only slightly by 9% in germinated beans and 15% in fungus-stress germinated samples, respectively. The advantage of stress germination of soybeans in enriching phytoalexins is traded off by loss of tocopherols.