The identification and validation of genetic factors ('biomarkers') that reliably predict the efficacy and toxicity of specific pharmacological agents for individual patients would significantly improve the current treatment of patients with epilepsy. A pharmacogenetic biomarker classification has been proposed that identifies three biomarker types involved in drug response: 'known valid biomarkers', 'probable valid biomarkers' and 'exploratory or research biomarkers'. The only known valid antiepileptic drug biomarker is HLA-B*1502 (Stevens-Johnson syndrome in patients of specific Asian backgrounds taking carbamazepine). Probable valid antiepileptic drug biomarkers include polymorphisms in one drug transporter gene, two drug metabolizing genes, three sodium channel genes and one HLA allele. Current methodological challenges to identifying new antiepileptic medication biomarkers can only be overcome with large-scale collaborative research efforts.