Prenatal diagnosis of major congenital anomalies and subsequent termination of affected pregnancies has been widely available as part of routine obstetric care in recent years. In this study, vital statistical data on stillbirths, live births, and infant deaths were used to examine secular trends in gestational age-specific and category-specific fetal and infant mortality due to congenital anomalies in Canada (excluding Ontario and Newfoundland) from 1985-1996. Comparisons of the rates between 1985-1987 and 1994-1996 were made using relative risks and 95% confidence intervals (CI). The overall fetal mortality rate due to congenital anomalies increased significantly, from 68.0 per 100,000 total births in 1985-1987 to 78.6 per 100,000 total births in 1994-1996, while the overall infant mortality rate due to congenital anomalies decreased significantly over the same period, from 2.47 to 1.79 per 1,000 live births. The fetal death rate due to congenital anomalies at 20-21 weeks of gestation increased approximately five-fold (relative risk [RR] = 4.83, 95% CI = 3.28-7.11) from 4.5 to 21.5 per 100,000 fetuses at risk, while the rate at 37-41 weeks decreased by 30% (RR = 0.70, 95% CI = 0.50-0.97). Fetal death rates among pregnancies at 20-25 weeks of gestation increased in all categories of congenital anomaly except anencephaly and respiratory system anomalies. Congenital anomaly-related fetal and infant deaths have increased at early gestation but declined at later gestation in Canada. These changes suggest an increase in prenatal diagnosis and selective termination of pregnancies with congenital anomalies in recent years.