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Background: The effects of folic acid fortification on neural tube defects is well known. Other reports show a beneficial effect of the fortification on orofacial clefts, urinary malformations and defects caused by limb reduction., Aim: To determine the changes in prevalence of congenital malformations after the start of flour folic acid fortification in Chile., Material and Methods: The rates of 22 malformations occurring in the maternity of the University of Chile Clinical Hospital and other Chilean hospitals participating in the Latin American Collaborative Study of Congenital Malformations (ECLAMC) were compared before and after the start of flour folic acid fortification., Results: After the start of folic acid fortification a significant reduction in the rates of anencephalia, spina bifida and diaphragmatic hernia, was observed. The rates of all other malformations remained stable or increased. The rates of all malformations at the University of Chile Clinical Hospital had a steady increase until 2005 and were significantly higher than in the rest of hospitals participating in ECLAMC., Conclusions: Folic acid fortification was associated with an expected reduction in rates of spina bifida and anencephalia and an unexpected reduction in the rates of diaphragmatic hernia.