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Introduction: Despite improving maternal-child indicators in Brazil, congenital malformations are still the second cause of mortality in the first years of life. This work aims to compare statistical data before and after flour fortification with folic acid (FA) in Brazil., Methods: A cross-sectional Brazilian-population-based study compares the spina bifida (SB) rates pre- and post-fortification of the flour with folate. Data collected from the public database of the Live Birth Information System (SINASC/SUS) was performed. The period 1999-2004 (pre-fortification) was compared with 2005-2010 (post-maize and wheat fortification with FA), and another analysis comparing 2005-2010 and 2011-2020 (cassava flour fortification) was performed. The estimator was the prevalence ratio (PRR); the confidence interval selected was 95%. We used a random effects analysis model and inverse variance., Results: The review showed a tendency to decrease the PRR after flour fortification; however, there is no statistical significance between studies. DATASUS data analysis comparing 5 years before and 5 years after mandatory maize and wheat flour fortification demonstrated a rate ratio of 1.05 (95% CI 0.99-1.1; p = 0.075). Furthermore, comparing 10 years after additional cassava flour folate fortification, the rate ratio increased to 1.4 (95% CI 1.34-1.45; p < 0.01)., Conclusion: This study demonstrated an increase in SB after FA fortification. Possible explanations rely on national registry improvement, not fortified staple food, or further unidentified causes. Moreover, suggestions can be made for creating a mandatory registry for malformations, inspecting the concentrations of FA in the flour, and fortifying all food., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)