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Objective We assessed the effect of a daily intake of a micronutrient-fortified beverage for 14 mo on indicators of biochemical status of important micronutrients in schoolchildren. Methods A double-blind, placebo-controlled, matched-pair, cluster, randomization study design was used. Biochemical indicators of micronutrient status were evaluated at baseline and at the end of 14 mo on a subsample in nine matched pairs. Prevalence (percentage) of subclinical deficiency, mean, and mean increments of each indicator were compared between supplemented and placebo groups. Results Extent of inadequacy at baseline was more or less 100% for folic acid, 65% for vitamins B2 and B6, and 55% for vitamins C and A. Prevalence of anemia among subjects was 55%, with inadequacy of vitamin B12 being 40% and that of vitamin D being 30%. No subject had inadequacy of iodine based on urinary iodine. Supplementation of a micronutrient-enriched beverage for 14 mo significantly improved the status of many of the nutrients. The effect was significant with respect to vitamins A, B2, and B12, folic acid, vitamin D, parathyroid hormone, and thyroid-stimulating hormone in children who received the supplement compared with those who received only placebo. Hemoglobin status improved only in children who had anemia in the supplemented group. Conclusions Prevalence of multiple subclinical micronutrient deficiencies are high in middle-income Indian school children. Daily consumption of a micronutrient-enriched beverage had positive effects that were confined to those nutrients that were inadequate at baseline.