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Maternal use of antiepileptic drugs (AEDs) during pregnancy has been associated with an increased risk of congenital abnormalities in the fetus. This is partly attributable to AEDs. We aimed to analyse seizure frequency and the rate and type of any congenital malformation related to pregnancies in women with epilepsy in this prospective study. Eighty four pregnant women with epilepsy on AEDs were followed for congenital malformations. Z test was used for statistical analysis. Pregnancy did not influence the seizure frequency in 64 (76.2%) pregnancies. The seizure frequency increased in 16 (19.04%) pregnancies. In 4 (4.76%) pregnancies the number of seizures decreased during pregnancy. Overall percentage of congenital malformations in infants of mothers with epilepsy treated with AEDs was 10%, versus 3.65% in the general Turkish population. Percentages of malformations in children of pregnancies in women with epilepsy on antiepileptic drugs (AEDs) were; 6.52% (3/46) for carbamazepine (CBZ), 14.28% (2/14) for phenytoin (PHT), 13.33% (2/15)for valproic acid (VPA) and 20% (1/5) for phenobarbital (PB). This comfirms previous reports that all four AEDs (CBZ, PHT VPA, PB) are associated with an increased risk of congenital malformations, although CBZ seems to be the the safest agent in monotherapy.