To assess the extent that early mortality syndrome (EMS) impacts different Pacific salmonid stocks and the association of EMS with thiamine, we collected eggs of coho salmon Oncorhynchus kisutch from three Lake Michigan tributaries (Platte River, Thompson Creek, and Root River) in 1996-2001. We also obtained eggs of Chinook salmon O. tshawytscha from Lake Michigan (Little Manistee River) and Lake Huron (Swan River) in 1998-2001. Unfertilized eggs from individual females were frozen for thiamine analysis, and the remainder were fertilized and reared until first feeding. We observed a high incidence of EMS in offspring when total egg thiamine levels were less than 1.7 nmol/g in both coho and Chinook salmon. In Lake Michigan strain coho salmon from the Platte River, EMS occurred in more than 70% of monitored families in 1996, 1999, 2000, and 2001, while 1997 and 1998 were years when EMS was low (<25%). Hinchenbrooke strain coho salmon from Thompson Creek exhibited greater impacts from EMS in the years when EMS was low in the Lake Michigan strain coho salmon from the Platte River. Similar to coho salmon, Lake Michigan Chinook salmon also exhibited EMS (>70%) in 1999, 2000, and 2001. Chinook salmon from Lake Huron exhibited high (>70%) EMS in 2001, moderate (40-60%) EMS in 1999, and low (<25%) EMS in 1998. Our data suggest that the incidence of EMS in salmonids varies by species, location, and year. The data support the general contention that EMS in salmonids is associated with low egg thiamine content. ?? Copyright by the American Fisheries Society 2005.