Background : Among all childhood seizure patients febrile seizure accounts for more than 30% of  the total. A lot of confounding factors are there in the causation of febrile seizure. We designed this study to investigate the mutation in cytokine gene to determine whether this polymorphism could be a marker of susceptibility to febrile seizure in children. Materials and methods: 100 case and 100 age and sex matched healthy controls were selected. Fasting blood samples were collected. Data was analyzed statistically.Results: Genetic variations in cytokine gene  was found among the febrile seizure patients. Discussion: Any mutation in the coding region of  cytokines might effect their production and  resulted in febrile seizure. Conclussion: Treating the patient a gene analysis may give prior information and can decrease the morbidity and future complications to the patient and the related family members.