Although pyridoxine-dependent seizures have been reported for decades, pyridoxamine phosphate oxidase deficiency has only been recently described. Pyridoxamine phosphate oxidase (PNPO) is one of a series of enzymes involved in converting pyridoxine to pyridoxal 5′-phosphate, the biologically active form of pyridoxine. PNPO deficiency is associated with decreased levels of pyridoxal 5′-phosphate in CSF, as well as epilepsy. We describe four children up to 16 years of age with intractable seizures who all had low cerebrospinal fluid (CSF) levels of pyridoxal 5′-phosphate. Only one of the four children possessed a genetic alteration, a novel homozygous variant in exon one of the PNPO gene. Three of four, however, showed at least some clinical improvement with pyridoxal 5′-phosphate supplementation. Low CSF pyridoxal 5′-phosphate levels, although considered a diagnostic biomarker for PNPO deficiency, lack specificity and may result from multiple other causes. Genetic testing and CSF evaluation, along with clinical response are all necessary for accurate diagnosis. © 2013 Elsevier Inc. All rights reserved.