Introduction: Zinc (Zn) is an essential micronutrient for cell growth, protein synthesis and cell differentiation. This deficiency affects the growth, development, energy metabolism and immune response in Colombian children's. Objective: To examine factors associated with Zn deficiency in a representative sample of Colombian children. Patients and methods: A cross-sectional descriptive study was conducted of data from the 2010 National Nutrition Survey of Colombia (ENSIN 2010), in 4.279 children aged between 12-59 months of age. Plasma levels of Zn were determined by atomic absorption spectrophotometry, and associated factors (sex, age, ethnicity, SISBEN score, and geographic region) were collected by structured questionnaire. Associations were established through a multivariable regression model. Results: We found a range of Zn of 78.5 μg/dl, (95% CI 76.7 to 80.4 μg/dl). 43.3% (95% CI 42.2%-44.3%) of children had lower Zn levels to 65 μg/dl. Children belonging to an ethnic groups (indigenous) or residing in rural areas; showed Zn deficiency (56.3% and 47.8%) respectively. Regression models show that to be indigenous (OR 1.76, 95% CI 1.29 to 2.41), and to reside in rural areas (OR 1.39, 95% CI 1.16 to 1.67) were associated with Zn deficiency. Conclusions: The study population shows a high prevalence of Zn deficiency, so it is recommended that comprehensive interventions which are involved nutritional and educational component.