Polygonum cuspidatum is a potent anti-oxidant herb that is well known for its various bioactivities. The current study investigates which compound group is most effective, to establish the key compound groups for quality assessment, especially in terms of neuroprotective effects. The roots of P. cuspidatum were extracted with 85% methanol and fractionated with hexane, ethyl acetate, n-butanol and water. Each fraction was applied to an in vitro radical scavenging assay, a lipid peroxidation assay in brain homogenates and an in vivo assay using a transient focal cerebra ischemia model induced by a middle cerebral artery occlusion in a Sprague-Dawley rat. The ethyl acetate fraction was the most effective fraction in both in vitro and in vivo assays, having the highest stilbene and anthraquinone contents. These results suggest that stilbenes and anthraquinones may be key compound groups for the quality assessment of the anti-oxidative and neuroprotective effects of P. cuspidatum.