Technical Abstract: Polar lipid peroxidation and vitamin E concentrations were determined for kidney and liver tissues of chinook salmon Oncorhynchus tshawytscha sampled before release from three hatcheries in the Snake River Basin, Idaho, and from juvenile-fish bypass systems at several dams in the Columbia-Snake River Federal hydropower system. Generally, lipid peroxidation increased and vitamin E decreased as the juveniles migrated downstream in each of the study years (1999 and 2000). The largest increase in liver lipid peroxidation occurred between the hatcheries and Lower Granite Dam, the first dam encountered by migrating fish, with little or no additional change as the fish migrated through the hydropower system. Kidney lipid peroxidation, on the other hand, continued to increase as the fish migrated to dams on the lower Columbia River, 348 to 461 km further downstream. Decreases in vitamin E were significant for liver tissue in 2000 and for kidney tissue in 1999. Liver and kidney lipid peroxidation indices were higher and vitamin E concentrations lower in 1999 than in 2000, possibly because river flows, spill levels at the dams, and dissolved gas levels in the river were higher in 1999. Liver vitamin E was significantly lower in fish exposed to juvenile-fish bypass systems at two or more dams (including the dam where they were sampled) than in fish bypassed only at the sampling location; greater exposure to bypasses did not, however, increase liver or kidney peroxidation indices. Increased polar lipid peroxidation could potentially have adverse effects on a range of physiological processes in migrating smolts, including processes involved in acclimation to sea water.