Objective: To compare the contents and transfer rate of hazardous substances in crude, washing solution, crude after washing, decoction and remnant after boiling. Methods: The heavy metal contents of each step were measured by inductively coupled plasma mass spectrometer (ICP-MS) and mercury analyzer (SP-3DS). In order to analyze pesticides in each sample we used simultaneous multi-residue analysis of pesticides by GC/ECD, which was followed by GC/MSD analysis to confirm the identity of the detected pesticide in each sample. In addition, the contents of sulfur dioxide ($SO_2$) were performed by Monier-Williams distillation method. Results: 1. Contents (mg/kg) of heavy metals were not detected in decoctions of any tested herbal medicine prescriptions. 2. Transfer rates (%) of heavy metals from crude to remnant were as follows: Yijin-tang (As: 46.9, Cd: 50.0 and Pb: 100.0), Oryung-san (As: 80.0, Cd: 100.0 and Pb: 73.8), Hwangryunhaedok-tang (As: 88.9, Cd: 71.4 and Pb: 92.7), Bangpungtongseong-san (As: 100.0, Cd: 17.3 and Pb: 56.1), Oyaksungi-san (As: 47.4, Cd: 175.0 and Pb: 142.4). 3. Contents (mg/kg) of residual pesticides were not detected in any samples. 4. Transfer rate (%) of sulfur dioxide ($SO_2$) from crude to remnant in all samples were as follows: Yijin-tang (25.0), Oryung-san (166.7), Hwangryunhaedok-tang (50.0), Bangpungtongseong-san (181.8), Oyaksungi-san (50.0). Conclusion: Our results showed that the boiled herbal medicine prescriptions which we take are safe from the hazardous substances.