Baller-Gerold syndrome (BGS) is characterized by craniosynostosis and preaxial upper-limb malformations, and it has an autosomal recessive inheritance. Valproate syndrome occurs after exposure to valproic acid in utero, and is characterized by trigonocephaly. Both syndromes can also present with other malformations. Herein, we report a female newborn and her brother who both had a history of fetal exposure to maternal anti-epileptic drugs, especially sodium valproate. On physical examination of the female patient, craniosynostosis, trigonocephaly, right radius aplasia and hypoplastic thumb, and cardiac and renal malformations were determined, and she was diagnosed with BGS phenotype. The brother's examination revealed trigonocephaly, polymastia and hypospadias, and he was diagnosed with valproate syndrome. Based on these patients, we aimed to add further evidence in the literature indicating that the use of sodium valproate alone and in combination with other anti-epileptic drugs throughout pregnancy can increase the risk of serious fetal congenital malformations depending on the doses.