Abstract Objective The anthraquinones (aloe-emodin, rhein, emodin, chrysophanol, and physcion) in Dahuang Huanglian Xiexin decoction (DHXD), a compound prescription consisting of Rhizoma Rhei, Rhizoma Coptidis, and Radix Scutellariae were to be determined in this study. Methods An HPLC method with UV detection was developed and validated. Results The UV response of the HPLC method was found to be linearly related to the concentrations of individual anthraquinones ranging from 3.15 to 64.00 μg.ml-1 for aloe-emodin, rhein, emodin, and chrysophanol, and from 1.70 to 33.92 μg. ml-1 for physcion. The average extraction recovery was about 102%. However, different amounts of anthraquinones were found in the decoctions prepared from the single herb Rhizoma Rhei, as well as Rhizoma Rhei in combination with Rhizoma Coptidis or Radix Scutellariae, and DHXD. Conclusions These results show that the levels of anthraquinones in different Rhizoma Rhei decoctions can be significantly altered by Rhizoma Coptidis and/or Radix Scutellariae.