Baltic salmon suffer from maternally transmitted yolk-sac fry mortality syndrome—M74. The incidence of M74 varies considerably on a year to year basis. In the 1990s the mortalities were 50–80% but in 2003–2005, below 10%. Before death, M74-affected fry have several typical symptoms. M74-eggs are characterized by low thiamine and carotenoid content, and affected fry show signs of oxidative stress. Although M74 is associated with thiamine deficiency and the symptoms of the fry can be alleviated with thiamine, the underlying causes of the syndrome have remained a mystery. We have studied the symptoms of M74 at the molecular level by investigating the global gene expression patterns using cDNA microarray and have quantified the changes in transcriptional regulation in M74-affected and healthy yolk-sac fry. Our and previous results suggest that M74 in Baltic salmon yolk-sac fry results from oxidative stresses disturbing several different developmental molecular pathways. Because the M74 syndrome is of maternal origin, factors in the Baltic Sea during salmon feeding and migration, i.e., the chemical composition of food, may be decisive in the development of M74. The possible mechanisms by which oxidative stresses may develop in adult salmon are discussed in the review.