The effectiveness of flour fortification in reducing anaemia prevalence is equivocal. The goal was to utilise the existing national-level data to assess whether anaemia in non-pregnant women was reduced after countries began fortifying wheat flour, alone or in combination with maize flour, with at least Fe, folic acid, vitamin A or vitamin B12. Nationally representative anaemia data were identified through Demographic and Health Survey reports, the WHO Vitamin and Mineral Nutrition Information System database and other national-level nutrition surveys. Countries with at least two anaemia surveys were considered for inclusion. Within countries, surveys were excluded if altitude was not consistently adjusted for, or if the blood-draw site (e.g. capillary or venous) or Hb quantification method (e.g. HemoCue or Cyanmethaemoglobin) differed. Anaemia prevalence was modelled for countries that had pre- and post-fortification data (n 12) and for countries that never fortified flour (n 20) using logistic regression models that controlled for time effects, human development index (HDI) and endemic malaria. After adjusting for HDI and malaria, each year of fortification was associated with a 2.4% reduction in the odds of anaemia prevalence (PR 0.976, 95% CI 0.975, 0.978). Among countries that never fortified, no reduction in the odds of anaemia prevalence over time was observed (PR 0.999, 95% CI 0.997, 1.002). Among both fortification and non-fortification countries, HDI and malaria were significantly associated with anaemia (P,0.001). Although this type of evidence precludes a definitive conclusion, results suggest that after controlling for time effects, HDI and endemic malaria, anaemia prevalence has decreased significantly in countries that fortify flour with micronutrients, while remaining unchanged in countries that do not.