Introduction: To determine the relation of serum magnesium level with metabolic and clinical parameters in obese children. Materials and Methods: Children presenting with weight gain whose BMI was over 95th percentile (obese children) and children with BMI lower than 85th percentile (non-obese) were included to the study. Taking drugs or having a history or evidence of chronic diseases, syndromal or endocrine causes of obesity were excluded. Weight and height were measured for comparing the anthropometric values. For laboratory evaluation, fasting serum glucose, insulin, lipid profile and serum magnesium levels were measured. We compared the differences in between obese and lean groups with Student's t-test and Pearson's correlation analysis was used to compare the variables. The value of p<0.05 was considered statistically significant. Results: A total of 80 obese children (10.2±2.7 years of age, 40 male patients) and 60 age and gender matched lean children (10.9±2.6, years of age, 30 male patients) were included in this study. The obese subjects had significantly higher serum magnesium, insulin, HOMA-IR, total cholesterol, triglyceride, and HDL-cholesterol levels than the lean subjects (p<0.05), while there were no significant differences between glucose and LDL-cholesterol levels (p>0.05). In obese group serum magnesium level significantly correlated with only SDS-BMI (p<0.05), while there were no correlation between BMI, total cholesterol, triglyceride, HDL-cholesterol, LDL-cholesterol, fasting glucose, and insulin levels (p>0.05). Conclusions: In accordance with previous studies, the present study supports the finding that serum magnesium levels are lower in children with obesity compared to healthy controls. On the other hand, we did not find a correlation between serum magnesium levels and insulin resistance and lipid levels. In conclusion, obese children should ingest adequate a mounts of magnesium in order to prevent complications associated with low magnesium levels. © The Journal of Current Pediatrics, published by Galenos Publishing.