Anemia has been identified as a severe public health concern among young children in India, however, information on the prevalence of anemia attributed to micronutrient deficiencies is lacking. We aimed to assess multiple micronutrient status (iron, zinc, selenium, vitamin A, vitamin D, folate and vitamin B12) in young Indian children and to investigate the role of these seven micronutrients and other non-nutritional factors on hemoglobin concentrations and anemia. One-hundred and twenty children aged 12 to 23 months were included in a cross-sectional nutritional assessment survey, of which 77 children provided a blood sample. Hemoglobin (Hb), serum ferritin, soluble transferrin receptor (sTfR), total body iron, zinc, selenium, retinol binding protein (RBP), folate, vitamin B12 and 25-hydroxyvitamin D (25(OH)D) were measured, and adjusted for inflammation using C-reactive protein (CRP) and α-1-acid glycoprotein (AGP), where appropriate. Predictors for hemoglobin and anemia were identified in multiple regression models. Most of the children were classified as anemic, of which 86 to 93% was associated with iron deficiency depending on the indicator applied. Deficiencies of folate (37%), and notably vitamin D (74%) were also common; fewer children were classified with deficiencies of vitamin B12 (29%), zinc (25%), and vitamin A (17%) and selenium deficiency was nearly absent. Multiple micronutrient deficiencies were common with over half (57%) deficient in three or more micronutrients, and less than 10% of children were classified with adequate status for all the micronutrients measured. Iron status was found to be the only nutritional factor statistically significantly inversely associated with anemia (P = 0.003) in multivariate analysis after controlling for sex. A coordinated multi-micronutrient program is urgently needed to combat the co-existing micronutrient deficiencies in these young children to improve micronutrient status and reduce the high burden of childhood anemia.