Congenital hallux varus is a rare deformity of the great toe characterized by adduction of the hallux and medial displacement of the first metatarsophalangeal joint. Prenatal diagnosis of congenital hallux varus is presented herein. A 32-year-old woman was referred to our unit due to significant deviation of the fetal right great toe at 22+2 weeks of pregnancy. Ultrasound examination revealed a thick and short great toe, which was significantly angulated medially on the right side. Amniocentesis was performed and the result was reported as inv(9) (p11;q12). After delivery, the clinical examination confirmed the prenatal diagnosis. To our knowledge, this is the first reported prenatal diagnosis of an isolated congenital hallux varus. Congenital hallux varus can be diagnosed easily in the prenatal period by 2-D and 4-D ultrasonography. Prenatal karyotyping should be taken into consideration, especially in the presence of associated anomalies, such as polydactyly and clubfoot.