An assay for fondaparinux (Arixtra) is described based on a modified commercial assay for heparin. The assay is automated on a Dade Behring BCS XP (Siemens Healthcare Diagnostics, Deerfield, IL) and uses the inhibition of activated factor X to quantitate the drug. The assay was unaffected by platelet contamination or the presence of warfarin. The assay was affected by the antithrombin level, and the value obtained in the assay decreased significantly when the antithrombin level was less than 60%. The assay is, however, not specific for fondaparinux. Specimens containing unfractionated or low-molecular-weight heparin will yield results by this assay that will not be an accurate estimation of concentration.