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To combat iron and other micronutrient deficiencies, the Ministry of Health of the Kyrgyz Republic launched a regional Infant and Young Child Nutrition (IYCN) program in 2009, which included promotion of home fortification with micronutrient powder (MNP) containing iron (12.5 mg elemental iron), vitamin A (300 μg) and other micronutrients. Every 2 months children aged 6-24 months were provided 30 sachets to be taken on a flexible schedule. The objective was to assess biochemical indicators of iron and vitamin A status among children aged 6-24 months at the baseline and follow-up surveys.Cross-sectional representative cluster surveys were conducted in 2008 (n = 571 children) and 2010 (n = 541). Data collected included measurement of hemoglobin, serum ferritin, soluble transferrin receptor (sTfR), retinol-binding protein, C-reactive protein (CRP) and α1-glycoprotein acid (AGP).Among all children, declines were observed in the prevalence of: anemia, 50.6% versus 43.8% (P=0.05); total iron deficiency (either low ferritin or high sTfR), 77.3% versus 63.7% (P<0.01); and iron deficiency anemia, 45.5% versus 33.4% (P<0.01). Among children without inflammation as measured by CRP and AGP, similar declines were observed, but only declines in total iron deficiency and iron deficiency anemia reached statistical significance. Among all children and those without inflammation, the prevalence of vitamin A deficiency remained the same.One year after the introduction of home fortification with MNP, within a larger IYCN program, the prevalence of anemia, iron deficiency and iron deficiency anemia declined, but vitamin A deficiency remained unchanged.