This study was performed to investigate contamination levels of aflatoxins, the secondary metabolites produced by fungi Aspergillus flavus and A. parasiticus, in herbal medicine. Herbs is susceptible to these fungi infections through its growth harvest, transport and storage. This study determine the aflatoxin B₁, B₂, G₁ and G₂levels by HPLC-florescence detector coupled with photochemical enhancement in 558 samples herbal medicine distributed in Korea and China. Also, We checked a transfer ratio of aflatoxins from raw herbal medicines to herbal medicine extract. Hot water extraction of herbal medicines was prepared by air pressure and high pressure condition. The analytical method for aflatoxins was validated in this method. In results recoveries of the analytical method were ranged from 67.4% to 96.2% and, limits of detection and quantitation for aflatoxins were 0.015~0.138 μg/kg and 0.046~0.418 μg/kg, respectively. According to the results of monitoring on aflatoxins in herbal medicine, aflatoxins 1.7 ug/kg B1 and 0.9 ug/kg G₁were detected in only one sample of Strychni Ignatii Semen, and 0.8 ug/kg G₁ in Strychni Semen. About 13.6~51.3% of aflatoxins were transferred to hot water extract. Although the detected levels are under the permitted levels for aflatoxins in herbal medicine, these amounts should be considered in regard to overall daily exposure to mycotoxins.