Objective In this study, we aimed to assess the association between four variants in three genes whose association has been reported in adults but not in children. We evaluated the relationship of the GCKR (rs780094), GCKR (rs1260333), FADS (rs174547), and MLXIPL (rs3812316) polymorphisms with serum lipid levels in Iranian children. Design This cross-sectional study was conducted in a subpopulation of the CASPIAN III study. During this study, 550 frozen whole blood samples were selected randomly. Using the recorded information of selected cases, those with and without abnormal lipid levels were determined. Allelic and genotypic frequencies of GCKR (rs780094), GCKR (rs1260333), MLXIPL (rs3812316), and FADS (rs174547) polymorphisms were determined and compared in dyslipidemic and normal children. The association between the studied polymorphisms and lipid profiles was determined using logistic regression analysis. Results Prevalence of hypercholesterolemia, hypertriglyceridemia, high low-density lipoprotein cholesterol (LDL-C), and low high-density lipoprotein cholesterol (HDL-C) were 24.9, 34.5, 19.0, and 40.7%, respectively. Significant correlations were found between GCKR (rs780094) and GCKR (rs1260333) polymorphisms and cholesterol and triglyceride levels, between FADS (rs174547) polymorphism and level of triglyceride, and also between MLXIPL (rs3812316) and levels of HDL-C. Conclusions The results of this population-based study provide evidence for a relationship between lipid regulatory gene polymorphisms including GCKR (rs780094), GCKR (rs1260333), FADS (rs174547), and MLXIPL (rs3812316) with dyslipidemia in an Iranian population. These results could provide baseline information on as well as further insight into the genetic makeup of lipid profiles in Iranian children, which could be used for preventative strategies.