Epilepsy is one of the most common neurological disorders, nearly 70% of patients with epilepsy lack an obvious pathogenetic cause, genetic is believed to play an important role in its causation. Objectives: to determine the association of sodium channel SCN1A gene mutation with epilepsy. Methods: The current study is a cross-sectional study that had been performed at Sheikh Mohamed Khair centre, Banat, Omdurman, and National Centre for Neurological Sciences (NCNS) Khartoum state, during the period November 2016 to February 2019. Ninety-nine patients were enrolled in this study. Demographic data were collected in a predesigned questionnaire. Blood samples were tested for biochemical and molecular tests. Results: sequencing analysis detected AT deletion in 71% of the samples. Conclusion: Genetic mutations have an effective role in developing epilepsy, AT deletion in SCN1A gene, indirectly, affects Gamma aminobutyric acid function which is inhibition of neuronal activity.