Children of epileptic mothers have a greater risk for congenital malformations than is seen in the general population. This risk has been attributed mostly to teratogenic effects of antiepileptic drugs, but other risk factors have been suggested, such as epilepsy, per se, or some underlying genetic defects associated with epilepsy. Previous studies do not answer the question of whether genetic factors contribute to the high risk of malformations in children of epileptic parents. Genetic studies in families of patients with neural-tube defects and cleft lip (CL), with and without cleft palate (CP), as well as genetic studies in families of patients with epilepsy, show evidence for the possible existence of genes on the short arm of chromosome 6. The suspected gene for CL and CP is linked to factor XIIIa and is neither identical with or linked to a gene for idiopathic generalized epilepsy, which is close to the HLA region. The short arm of chromosome 6 also contains a human homologue of the mouse t-complex. Alterations of the mouse t-complex are involved in defects of neural-crest development in mice. Relationships between a human homologue of the mouse t-complex, epilepsy, and birth defects have yet to be proven.