Objectives: Fortification of grain products with folic acid has been shown to significantly reduce the occurrence of neural tube defects (NTDs) in Canada and elsewhere. However, the impact on non-NTD anomalies has not been well studied.Methods: Using the Alberta Congenital Anomalies Surveillance System (ACASS), we examined changes in occurrence of select congenital anomalies where folic acid supplementation with multivitamins had previously been suggested to have an effect. Anomalies documented in the ACASS 1992-1996 (pre-fortification) were compared to 1999-2003 (post-fortification).Results: A significant decrease in spina bifida (OR 0.51, 95% CI 0.36-0.73) and ostium secundum atrial septal defects (OR 0.80, 95% CI 0.69-0.93) was evident, but there was a significant increase in obstructive defects of the renal pelvis and ureter (OR 1.45, 95% CI 1.24-1.70), abdominal wall defects (OR 1.40, 95% CI 1.04-1.88) and pyloric stenosis (OR 1.49, 95% CI 1.18-1.89). Conclusions:Consistent with other studies, a 50% reduction in spina bifida was associated with the post-fortification time period. Supporting the possibility that folic acid fortification may play a role in preventing other birth defects, a 20% reduction in atrial septal defects was also associated. The increase in abdominal wall defects, most notably gastroschisis, is likely related to pre-existing increasing trends documented in several regions around the world. The increase in pyloric stenosis and obstructive urinary tract defects was not expected and any causal relationship with folic acid fortification remains unclear. Similar studies by other birth defects surveillance systems in Canada and elsewhere are needed to confirm these trends.