Ischemic stroke is a significant health condition, whose frequency in childhood is increasing day by day. Although many factors are effective in development of the stroke, it has been showed that individuals having risk factors have a genetic predisposition. The aim of the study is to determine whether distinct genetic mutations are risk factors for children with history of ischemic stroke. Our sample data is taken from 58 patients (29 male and 29 female) who applied our hospital between 2012 and 2016 with diagnosis of acute or chronic arterial stroke and from 70 healthy children (32 male and 38 female) with similar particularities in the sense of age and sex, who have not any chronical disease. Blood samples are taken from each child participated in the study to conduct genetic analysis. It has been examined whether a mutation exists in gene locations of CDKN2B-AS1 (Rs2383206), HDAC9 (Rs11984041), NINJ2 (Rs12425791), NAA25 (Rs17696736). Moreover, whether there are significant difference between patient and control group has been investigated. In the genetic analysis of patients and control groups, no significant difference has been found for any of the genes. Mutations in gene locations of CDKN2B-AS1 (Rs2383206), HDAC9 (Rs11984041), NINJ2 (Rs12425791), NAA25 (Rs17696736) are not risk factors for ischemic stroke in childhood. However this study showed us, the patients who inherit CDKN2B-AS1 and HDCA9 gene mutations had poor prognosis. However, this study should be replicated for a wider sample of patient population.