High-performance ion chromatography and inductively coupled plasma–mass spectrometry methods have been applied to estimate the content of Cd, Co, Cu, Fe, Mn, Zn, and Ni in whole blood, plasma, and urine of obese and nonobese children. The study was conducted on a group of 81 Polish children of age 6–17 years (37 males, 44 females). Obese children were defined as those with body mass index (BMI) >95th percentile in each age–gender-specific group. Statistical testing was done by the use of nonparametric tests (Kruskal–Wallis's and Mann–Whitney's U) and Spearman's correlation coefficient. Significant correlations appeared for control group in plasma (Mn–Cd, Ni–Co), urine (Cu–Co), and blood (Fe–Cu), while for obese patients in plasma (Cd–Mn, Ni–Cu, Ni–Zn) and urine (Fe–Cd, Co–Mn). Sex criteria did not influence correlations between metals' content in plasma and urine of obese patients. Metals' abundance was correlated in non-corresponding combinations of body fluids. Rare significant differences between content of metals according to sex and the type of body fluids were discovered: Zn in plasma from obese patients of both sexes, and Zn, Co, and Mn in blood, Mn in plasma from healthy subjects. Negative correlations between BMI and Zn in blood, Cu in plasma, and Fe in urine were discovered for girls (control group). Positive correlation between Co content in plasma and BMI was discovered for obese boys. The changes in metals' content in body fluids may be indicators of obesity. Content of zinc, copper, and cobalt should be monitored in children with elevated BMI to avoid deficiency problems.