The objectives of this study were to examine the effect of thiamine immersion of fish from a population known for compromised survival as a result of early mortality syndrome (EMS) and to investigate the cause-response relationship between thiamine concentration and lesions in tissues in swim-up-stage lake trout Salvelinus namaycush alevins. Lake trout eggs from 14 fish from Lake Michigan were artificially fertilized and the progeny divided into two groups based on the thiamine concentration (low [< 0.73 nmol/g] or high [> 0.85 nmol/g]) in the unfertilized eggs. Progeny were treated or not with a thiamine solution (2,000 mg/L for 2 h) at hatching or the swim-up stage. The survival of progeny in control groups at the swim-up stage correlated with thiamine concentration. The low thiamine-treated groups had significantly higher survival between the swim-up stage (812.0 degree-days) and 16 d after swim-up (963.3 degree-days) than the control groups; the survival of the high thiamine-treated groups did not differ between treated and control fish, regardless of the treatment at hatching and the swim-up stage. Control alevins that had low thiamine levels showed EMS, which resulted in 94.9-100% mortality 16 d after the swim-up stage. No pathological changes were observed in the brain, olfactory lobe, eye, liver, or muscle in alevins of high thiamine-treated group. Glycogen deposits in the liver of alevins from the low control group were variable, no glycogen being observed in the hepatocytes of 7 of the 24 fish. We demonstrate that thiamine treatment at swim-up enhances the survival of EMS-affected lake trout relative to treatment at hatching.