IntroductionCongenital malformations of the central nervous system (CNS) are morphological abnormalities of the brain and spinal cord that occur during fetal development. They constitute the second most common congenital disability, after congenital cardiac defects. Many risk factors have been identified; however, these studies included various types of congenital abnormality. Furthermore, there is a lack of information on risk factors for congenital CNS malformation, and notably in the Zinder region of Niger. ObjectiveThis study aimed to identify the risk factors associated with congenital CNS malformations in the Zinder region. MethodsIn a case-control design, patients with congenital CNS malformation were enrolled between June 2022 and April 2023 in the Department of Neurosurgery of the National Hospital of Zinder. ResultsFamily history of malformation (aOR:3.31, 95% CI:1.25−8.78) and consanguine marriage (aOR:2.28, 95% CI:1.23−4.20) were significantly associated with congenital CNS malformation. In contrast, folic acid supplementation (aOR:0.34, 95% CI:0.13, 0.89), multiparity (aOR:0.34, 95% CI:0.13, 0.89), and grand multiparity (aOR, 0.47; 95% CI:0.23, 0.97) had a protective effect. ConclusionRisk factors such as family malformation history and consanguine marriage increased the risk of developing congenital malformations of the central nervous system. In contrast, folic acid supplementation in the index period and multiparity had a significant protective effect.