Background: Vitamin D (VitD) deficiency is a common worldwide problem. Some previous studies have shown that both Zinc (Zn) and VitD deficiency are prevalent in Iran. This study aimed to assess the relationship of serum Zn and vitamin D levels in a nationally representative sample of Iranian children and adolescents. Methods: This case-control study was conducted as a sub-study of a school-based surveillance program entitled "the CASPIAN-III Study". An equal number of individuals with and without hypovitaminosis D including 330 participants aged 10 to 18 years were selected. The correlation of serum 25 hydroxy vitamin D (25(OH) D), cardiometabolic factors and Zn concentrations was determined. Statistical analysis was done using one-way analysis of variance (ANOVA), Pearson's correlation, linear regression, and logistic regression. Results: The mean age was not significantly different in participants with and without hypovitaminosis D (14.74±2.52 vs. 14.74±2.66 years, respectively, p>0.05). The mean 25(OH) D level was 6.34±1.47ng/ml in the group with hypovitaminosis D and 39.27±6.42ng/ml in controls. The mean Zn level was significantly lower in the hypovitaminosis D group than in controls (1.15±0.26 vs. 1.43±0.32μg/ml, respectively, p<0.001). The Pearson's analysis showed a positive and significant correlation between Zn and 25(OH) D serum levels (p<0.0001). Odds ratios analysis for VitD level between various quartiles of serum zinc concentration for all participants showed that the odds of higher levels of VitD increased by higher levels of Zn. Conclusion: We found significant associations between low serum concentrations of zinc and 25(OH) D. Food fortification or mineral supplementation should be considered in future health programs.