Prenatal diagnosis and termination of affected pregnancies can prevent infant deaths due to congenital anomalies, but an effect at the population level has not been shown. To examine the impact of recent changes in congenital anomaly-related fetal and infant deaths on overall population-based infant mortality. Birth cohort-based study of all live births, stillbirths, and infant deaths in Canada (excluding Ontario) for 1991-1998. Cause-specific infant mortality rates and gestational age-specific fetal death rates. The birth cohort-based infant mortality rate fluctuated between 6.4 and 6.1 per 1000 live births between 1991 and 1995, then dropped to 5.4 per 1000 in 1996 and 5.5 per 1000 in 1997. The rate of infant death from congenital anomalies was stable between 1991 and 1995 but declined by 21% (95% confidence interval, 19%-32%) from 1.86 per 1000 in 1995 to 1.47 per 1000 in 1996 and 1997. Fetal deaths due to pregnancy termination at 20 to 23 weeks' gestation increased dramatically in 1994, while fetal deaths due to congenital anomalies at 20 to 21 weeks increased in 1995 and subsequently. Provinces/territories with high rates of fetal death due to pregnancy termination/congenital anomalies at 20 to 23 weeks had fewer infant deaths due to congenital anomalies. A large decrease in infant deaths due to congenital anomalies was associated with the most recent decline in infant mortality in Canada, suggesting that increases in prenatal diagnosis and pregnancy termination for congenital anomalies are related to decreases in overall infant mortality at the population level.