Introduction: Obesity may be a risk factor for mineralisation and bone structure disorders, contrary to a common belief in its protective effects on bone tissue. Aim: The aim of the study was to assess the relationship between selected risk factors and obesity indicators and bone mass in obese children. Material and methods: The study included 80 children aged between 7 and 10 years with excessive body weight (60 obese and 20 overweight); the reference group included 37 children with body weight appropriate for height. All patients underwent physical examination with anthropometric measurements. Parents were asked to complete a questionnaire. The average daily intake of selected nutrients was analysed using Dieta 2 software package. Densitometry (dual-energy X-ray absorptiometry, DXA) was performed in all children to evaluate bone mass. Results: Obese and overweight children had statistically significantly higher total body BMD and total body BMD Z-score compared to control group. Most DXA parameters (except from volumetric bone mineral density) were positively correlated with body weight, height and waist circumference. A significant positive correlation was found between physical activity and total body BMD. There was a negative correlation between the average daily intake of proteins, carbohydrates, magnesium and phosphorus in obese children and most DXA parameters (p < 0.05). Conclusions: Bone mass in obese children is positively affected by somatic features (body weight, height, waist circumference and body composition) and physical activity, and negatively affected by increased intake of proteins, carbohydrates, phosphorus and magnesium. The calculated volumetric mineral bone density may reflect the actual bone mineral density and prevent DXA overestimation in obese children.