Salmonids in certain areas of North America and northern Europe suffer from reproductive disturbances manifested through the death of yolk sac fry. These disturbances are referred to as early mortality syndrome (EMS) in the Great Lakes region and M74 in the Baltic Sea. Both of these syndromes have been associated with reduced concentrations of thiamine in affected females and their eggs. However, large variations in signs and mortality, both within and between the individual syndromes, have been reported. Yolk sac fry mortality (M74) in Atlantic salmon Salmo salar has been shown to be associated with reduced DNA binding of the hypoxia-inducible transcription factor 1 (HIF-1), reduced production of vascular endothelial growth factor (VEGF) protein, decreased capillary density, and down-regulation of adult-type globin gene transcription (which is responsible for the protein part of adult hemoglobin). One of the main effects of all of these changes is reduced oxygen transport to the tissues of affected fry. In this study, the developmental patterns of HIF-1 DNA binding, VEGF protein expression, and adult-type globin gene transcription were analyzed in nine family groups of Lake Michigan lake trout Salvelinus namaycush. The results indicate that HIF-1 DNA binding and globin gene transcription increase from hatch to the end of yolk sac stage. Interindividual and between-family biological variations were detected, especially in VEGF protein expression and globin gene transcription. Our results demonstrate the possibility of using these molecular markers in investigating the etiology of EMS and making comparisons between the mechanisms of different salmonid yolk sac fry mortalities.