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Introduction: Obesity is primarily caused by the dysfunction of the energy homeostasis system. Numerous studies have reported an association between obesity and the rs17782313 variant near the melanocortin-4 receptor (MC4R) gene. In addition, the PKHD1 gene regulates the expression of fibrocystin. This gene is primarily expressed in the kidney and plays a role in fat and glucose metabolism. However, the interaction between PKHD1 polymorphisms and birth weight has not yet been investigated. This study showed the association between the rs17782313 variant near the MRC4 gene and rs2784243 in the PKHD1 gene amongst Iranian cases with obesity before maturity. Methods: One hundred and eleven Iranian patients and 100 healthy individuals aged 5 years and over were selected from the Tehran Moheb-e-Yas Hospital. Polymerase chain reaction-restriction fragment length polymorphism and sequencing methods were used for genotyping the genetic variants. A Chi-square test was applied to determine the association between rs17782313 and food intake and rs2784243 and birth weight. Results: The rs17782313 variant was associated with high food intake (P = 0.04), while the rs2784243 variant was associated with increased birth weight (P = 004). Conclusion: The MC4R rs17782313 and PKHD1 rs2784243 variants may contribute to food intake and early obesity. Moreover, a novel association was suggested between PKHD1 rs2784243 and birth weight.