Polygoni multiflori, one of traditional Chinese herbal medicines for the treatment of various diseases commonly associated with aging, is known to contain active anthraquinone ingredients. However, the content of the anthraquinones varies among P. multiflori samples with collection season and sites. Thus, simple, reliable and accurate analytical methods for determining of anthraquinones in P. multiflori products are needed for the quality control and pharmacological studies. To develop an HPLC method for the simultaneous determination of five anthraquinones, aloe-emodine, rheine, emodine, chrysophanol and physcione, in the roots of P. multiflori. Anthraquinones were extracted from the roots of P. multiflori using aqueous alcohol solutions or hot water under ultrasonication. Separation and quantitation of anthraquinones was accomplished using a reversed-phase C18 column with the mobile phase of methanol-water-phosphoric acid (600:400:1), and the detection wavelength of 254 nm. Seventy per cent aqueous ethanol showed the highest extraction efficiency for anthraquinones from roots of P. multiflori when compared with four other extraction solvents tested. All calibration curves were linear over the concentration range tested with the square of correlation coefficients >0.999. The detection limits (S/N = 3) were 0.89, 1.1, 1.6, 1.7 and 2.0 ng for chrysophanol, aloe-emodine, rheine, emodine and physcione, respectively. Emodine and physcione were found in the samples tested at concentrations of 0.341 and 0.197 mg/g, respectively. The described HPLC methods are simple, accurate and selective techniques for separation and quantification of anthraquinones in roots of P. multiflori and other plant samples.