A 2-year-old girl from a consanguineous marriage was evaluated for refractory seizures that had presented at birth. Since her presentation, she had been treated with pyridoxine and antiepileptic medications. Because she did not manifest the expected clinical response, pyridoxine was discontinued, which led to an increase in clinical events. Cerebrospinal fluid neurotransmitter metabolite chromatography and an assay of serum biomarkers, including pipecolic acid and α-aminoadipic semialdehyde, confirmed the diagnosis of pyridoxine-dependent epilepsy, and genetic testing identified a homozygous mutation in our patient, and in a first cousin with epilepsy. The reintroduction of pyridoxine and addition of folinic acid eventually led to control of her seizures. Early testing of biomarkers may prevent delays in diagnosing pyridoxine-dependent epilepsy. We recommend that all patients presenting with cryptogenic seizures before age 18 months undergo this evaluation.