Food fortification can be effective in reducing the prevalence of anemia and micronutrient deficiencies. This study assessed risk factors for-and the impact of the wheat flour program in Uzbekistan on-anemia, and iron and folate deficiency (FD) in non-pregnant women (NPW) of reproductive age. National data were analyzed for risk factors using multivariable regression. Additional iron intake from fortified flour was not associated with iron deficiency (ID) and did not result in a significantly different prevalence of anemia regardless of the levels, whereas women with additional folic acid intake had a lower relative risk (RR) of FD (RR: 0.67 [95% CI: 0.53, 0.85]). RR for anemia was greater in women with ID (RR: 4.7; 95% CI: 3.5, 6.5) and vitamin A insufficiency (VAI; RR 1.5; 95% CI: 1.3, 1.9). VAI (RR: 1.4 [95% CI: 1.3, 1.6]) and breastfeeding (RR: 1.1 [95% CI: 0.99, 1.2]) were associated with increased risk of ID, while being underweight reduced the risk (RR: 0.74 [95% CI: 0.58, 0.96]). Breastfeeding (RR: 1.2 [95% CI: 1.1, 1.4]) and inflammation (RR: 1.2 [95% CI: 1.0, 1.3]) increased risk of FD. FD results indicate that the fortification program had potential for impact, but requires higher coverage of adequately fortified wheat flour and a more bioavailable iron fortificant.