We aimed to assess element status in whole blood and tooth dentin and identify their correlations in overweight or obese children without additional metabolic risk factors. In a case-control study, 40 overweight and 80 normal weight children aged 6–10 years were enrolled. Samples of blood and tooth were collected. While all studied elements were similar in groups in univariate analysis, after adjustment for confounding factors, tooth Mn levels were lower and blood Zn levels were higher in the overweight/obese group (p = 0.049 and p = 0.032, respectively). A significant correlation in blood and tooth dentin levels of Sr and Zn was detected in both groups. In both biological substances, the concentrations of elements did not differ significantly in overweight children without metabolic comorbidities compared to healthy children of normal weight. Presence of low Mn levels in tooth dentin and high Zn levels in blood samples should be explored in further studies.