Background/Aims: Micronutrient deficiencies continue to be a major public health problem in India. The aim of this study was to assess the prevalence and determinants of micronutrient deficiencies among rural children. Methods: A community-based cross-sectional study was carried out by adopting a multistage stratified random sampling procedure. A total of 71,591 preschool children were included for ocular signs, 3,291 preschool children and 6,616 adolescents for hemoglobin, and 28,437 school-age children for iodine deficiency disorders. Results: The prevalence of Bitot's spots was 0.8% (CI = 0.6-0.9) and anemia among preschool children and adolescents was 67% (CI = 64.4-69.5) and 69% (CI = 67.0-71.4), respectively. The prevalence of total goiter was 3.9% (CI = 3.4-4.6). The risk of Bitot's spots was 2.4 times higher among preschool children of Scheduled Caste (SC) or Scheduled Tribes (ST) than others and risk of anemia was twice as high (CI = 1.5-2.6) among adolescents of SC and ST. The micronutrient deficiencies were significantly lower in children who used sanitary latrines. Conclusions: Micronutrient malnutrition is a public health problem among rural children, and it was higher among children of SC/ST, illiterate parents and those not possessing a sanitary latrine. Thus, there is a need to improve environmental sanitation; fortification of foods could also help in mitigating the problem.