Abstract Objectives To examine the burden of anemia, iron deficiency, and vitamin B12 deficiency in children under 5 in Mexico. Methods Data from the recently completed National Health and Nutrition Survey (ENSANUT 2018) were analyzed to examine the burden of anemia and micronutrient deficiencies in children under 5 (1 to <5 years). Hemoglobin (Hb) concentrations werequantified in capillary blood samples (n = 3144) via HemoCue.Venous blood samples (n = 1019) were collected, centrifuged, processed, and stored <−80°C until analysis of micronutrient biomarkers. Serum ferritin (SF), C-reactive protein (CRP), and vitamin B12 concentrations were measured via immunoassays. Hemoglobin was adjusted for altitude; anemia was defined as hemoglobin <11.0 g/dL. Iron deficiency was defined as serum ferritin <12.0 µg/L and iron insufficiency was defined as serum ferritin <20.0 µg/L; inflammation was defined as CRP concentrations > 5.0 mg/L (and CRP > 1.0 mg/L). Iron deficiency anemia was defined as hemoglobin <11.0 g/dL and serum ferritin <12.0 μg/L. Vitamin B12 deficiency and vitamin B12 insufficiency were defined as <148.0 and <221.0 pmol/L, respectively. Survey frequency procedures were used to examine the prevalence of anemia and micronutrient deficiencies; survey linear and logistic regression were used to examine associations of micronutrient biomarkers with hemoglobin concentrations and odds of anemia. Results A total of 22.9% of children were anemic in this population. In the biomarker sub-sample, 10.0% of children were iron deficient (SF < 12.0 µg/L), and 29.9% had serum ferritin concentrations <20.0 µg/L. A total of 9.5% of children had CRP concentrations >5.0 mg/L, and 34.7% had CRP > 1.0 mg/L. The prevalence of vitamin B12 deficiency (vitamin B12 < 148.0 pmol/L) was 5.4% and 21.5% of children had vitamin B12 insufficiency (vitamin B12 < 221.0 pmol/L). Conclusions Findings suggest that the burden of anemia and iron and vitamin B12 insufficiency is high in young children in Mexico. Funding Sources ENSANUT was funded by The Ministry of Health of Mexico.