Introduction. According to the data of the National Registry of Republic of Moldova, the incidence of congenital brain malformations (CBM) during 2010-2022 was 1.92 per 1000 newborns, accounting for 11% of all congenital anomalies. The objective of the study was to investigate the genetic polymorphisms involved in folate metabolism in mothers at risk of giving birth to children with congenital brain malformations. Material and methods. The target group included 105 children with a confirmed diagnosis of CBM. 50 mothers of children with CBM underwent molecular and genetic assessment, i. e. polymerase chain reaction for detection of four polymorphisms of the folate cycle genes. Statistical data processing was performed using the Quanto program. Results. The most common folate-dependent CBM diagnosed in heterozygous individuals after folate cycle genes was hydrocephalus, being revealed in 54 cases, polymorphisms in craniosynostosis - 15 cases, anencephaly and corpus callosum agenesis - 14 cases, encephalocele - 7 cases, meningoencephalocele - 3 and corpus callosum hypogenesis - 2 polymorphisms. Conclusions. The genetic polymorphism assay in folate cycle metabolism allows determining the genes associated with an increased risk of having children with CBM, which allows for its effective prevention.