Background: We aimed to evaluate apolipoprotein B-100 (APOB) EcoRI polymorphism and plasma lipid parameters together in children and adolescents. This is the first such study in Turkey to determine possible relationships of these parameters. Materials and Methods: Three separate groups were studied: a group of obese children with hyperlipidemia, a group of obese children without hyperlipidemia, and a group of health children neither with hyperlipidemia nor obesity. Polymerase chain reaction (PCR), denaturating gradient gel electrophoresis (DGGE) and automatic sequence analysis techniques were used. Sequencing results were examined by Proseq and BioEdit computer programmes. Results: Mutant A allele was not observed in the healthy control group, whereas it was more frequent in the hyperlipidemic obese children; the GA genotype was correlated with total and low density lipoprotein-cholesterol levels. Conclusion: In this study, we suggest that obese child patients having the A allele could have a higher risk for developing hyperlipidemia.