Abstract A reverse-phase HPLC method was developed for simultaneous quantification of six bioactive compounds in Rhizoma et Radix Polygoni Cuspidati. These compounds — polydatin (1), resveratrol (2), rhein (3), emodin (4), chrysophanol (5) and physcion (6) — were analysed from 24 authentic samples of the herb using UV HPLC. Based on the UV absorption characteristics of the six compounds, absorption wavelengths of 306 nm were chosen to quantify compounds 1 and 2, and 290 nm for compounds 3–6. A reliable and reproducible quantitative HPLC method for analysing authentic samples of Rhizoma et Radix Polygoni Cuspidati from different cultivation regions was developed. The results showed that the concentration of compound 1 in samples from Sichuan was almost 2-fold higher than that of samples acquired in Guangxi. Furthermore, compounds 3 and 5 were not found in all the samples tested. Thus, instead of using polydatin (1) and emodin (4) as markers for quality assessment, as in conventional practice, these findings show that compounds 2 and 6 are more suited to act as marker compounds for a more specific assessment of the quality of this herb.