Introduction . Childhood obesity has reached pandemic proportions, yet it remains unclear how genetic factors regulating bone metabolism influence the development of obesity and its metabolic complications, as well as bone mineral density in this group of patients. Aim. To establish associations between polymorphic markers of the VDR, CALCR, and COL1A1 genes and clinical phenotypes of obesity and their impact on bone metabolism in children. Materials and methods . A total of 99 obese children (54.5% boys, mean age 12.7 ± 3.6 years) and 61 healthy children (control group) were examined. A clinical and anamnestic examination, nutritional status assessment, biochemical analysis (lipid profile, carbohydrate metabolism), dual-energy X-ray absorptiometry (DXA) of the lumbar spine, and molecular genetic typing of CALCR (c.1340 C>T), COL1A1 (c.104-441G>T), and VDR (ApaI, c.1206T>C) polymorphisms using PCR and RFLP analysis were performed. Statistical analysis was performed using the Pearson χ² test and odds ratio (OR) calculation. Result. Carriage of the CC genotype of the CALCR gene was associated with obesity (OR = 11.667; p = 0.014), metabolic syndrome (OR = 3.895; p = 0.031), elevated LDL (OR = 6.833; p = 0.025) and hypertriglyceridemia (OR = 5.679; p = 0.014). The TT genotype of VDR ApaI was 2.6 times more common in children with obesity (OR = 2.644; p = 0.040). The GT genotype of the COL1A1 gene was associated with metabolic syndrome (OR = 3.339; p = 0.045) and hyper-LDL (OR = 3.304; p = 0.031), and the TT genotype was associated with hypertriglyceridemia (OR = 6.750; p = 0.044). In patients with normal bone mineral density (Z-score from -1 to +1), the GT COL1A1 genotype was more common (OR = 3.334; p = 0.037), while the CC CALCR genotype was associated with increased BMD (Z-score > +1), which may be compensatory. Conclusion . Polymorphic variants of bone metabolism genes significantly contribute to obesity, metabolic syndrome, lipid metabolism disorders, and bone mineral density in children. Identifying genetic risk groups may facilitate personalized prevention of complications.