A missense mutation in the gene encoding the alpha(2) subunit of the Na(+),K(+) ATPase pump (ATP1A2) was found in a family with both familial hemiplegic migraine (FHM) and Benign Familial Infantile Seizures (BFIC). As it is still unclear whether ATP1A2 is responsible for pure BFIC syndromes, we checked mutations of the ATP1A2 gene in probands of 12 Italian multiplex families with pure BFIC, who were negative for mutations in the SCN2A gene. We screened the ATP1A2 gene by denaturing high performance liquid chromatography (D-HPLC) and direct sequencing of DNA fragments showing an aberrant elution pattern. We found one exonic variant and five intronic variants, none leading to significant amino acid changes or causing a modification of the physiological mRNA maturation. The ATP1A2 gene does not appear to be involved in the ethiopathogenesis of pure BFIC syndromes, at least in the explored Italian multiplex families. It could be either responsible of a minority of cases, or of complex syndromes where BFIC and FHM co-occur.