One of the main attractions of treatment with herbal medicine is its apparent lack of side effects compared with the drug therapies used in allopathic medicine. However, evidence from various countries suggest that Asian herbal medicine carry a significant risk of contamination with toxic heavy metals at levels that may seriously threaten health. The aims of this study were to analyze and compare concentrations of heavy metals in urine and hair from 184 patients taking herbal medicines in the form of decoctions and/or pills in comparison to 101 control subjects taking either Western or no medications. Levels of metal concentrations exceeding WHO reference values were observed in a number of hair and urine samples for all subjects. After adjusting for potential confounders, taking decoctions or pills was associated with higher levels of some metals (such as Cu, Pb in urine), as well a higher odds ratio of exceeding the upper limit of reference ranges for Pb, Hg in hair. In contrast, taking decoctions or pills was associated with lower levels of some metals (such as Cu in urine and Cd, Cu, Hg, Pb in hair), suggesting that some herbal medicines may have a chelating effect on heavy metals in the body. Overall, the results obtained in the study show a mixed picture and suggest that heavy metals contamination in herbs is sometimes present, but may also be counteracted by the potential for some herbal medicines to act as chelating agents. Further study must be followed to obtain more concrete evidence.