Aim: The aim of our research is to study the relationship between the m.15452C>A variation in mitochondrial MTCYB gene and clinical findings of Turkish pediatric obese cases. The MTCYB gene encoded cytochrome b protein is one of the subunits of complex 3 which is localized in the ETS system. Complex 3 has an important function during the energy conversion which may contribute to obesity etiology. Material and Methods: Clinical and biochemical data (blood total cholesterol, triglyceride, HDL, LDL, glucose, insulin levels, HOMA-IR values and BMI Z-scores), and blood samples were collected for MTCYB gene analysis from unrelated 100 obese pediatric patients (BMI>95th percentile) and 100 nonobese (BMI between 5th and 85th percentile) healthy cases. MTCYB gene was sequenced using direct DNA sequencing analysis. The relationship between biochemical data and m.15452C>A variation was tested by t-test and Mann-Whitney U tests. Results: We found that 14 pediatric obese cases and 23 nonobese healthy cases had m.15452C>A variation. Obese cases who had m.15452C>A variation had higher blood HDL levels than other obese cases. Conclusion: The m.15452C>A variation may be related with a better plasma lipid profile in obese cases. Besides, current data provide an important step towards population genetics concerning its medical implications.