To test an association between environmental contaminants and the prevalence of congenital anomalies in colonial waterbirds, we collected representative eggs for chemical analysis from double-crested cormorant nests at colonies in Lake Michigan, Wisconsin, USA, and Lake Winnipegosis, Manitoba, Canada, and periodically revisited the nests to determine the hatching success, survivorship of hatchlings, and number of deformed hatchlings in the remainder of each clutch. Total concentrations of polychlorinated biphenyls (PCBs) in eggs were determined by capillary gas chromatography. The combined activity of planar chlorinated hydrocarbons (PCHs) in the eggs was measured in an in vitro bioassay based on the induction of ethoxyresorufin-O -deethylase (EROD) activity in rat hepatoma cells. The combined EROD induction activity was expressed as 2,3,7,8–tetrachlorodibenzo-p -dioxin equivalents (TCDD-EQ). Total concentrations of PCBs and TCDD-EQ were seven to eight times greater in eggs from Lake Michigan (7.8 μg/g and 138 pg/g, respectively) than in those from Lake Winnipegosis (1.0 μg/g and 19 pg/g, respectively). The proportion of eggs hatching at the Lake Michigan colony (59%) was less (p < 0.05) than at Lake Winnipegosis (70%), and the prevalence of hatchlings with deformed bills was greater (p < 0.001) at Lake Michigan (0.79 vs. 0.06%). However, within the Lake Michigan colony, concentrations of PCBs and TCDD-EQ were not correlated with either hatching success or the occurrence of deformities in nestlings.