The increase in the consumption of herb medicines have made their use a public health problem due to the potential fungal contamination and the risk of the presence of mycotoxins. 360 samples of herb medicines were evaluated for the aflatoxin contamination. The natural occurrence of aflatoxins in these samples were determined using immunoaffinity column clean up and high performance liquid chromatography (HPLC) with post-column derivatization. For samples analyzed, mean levels (incidence) of AFB1, AFB2, AFG1 and AFG2 in positive samples were 1.4 μg/kg (46.4%), 0.4 μg/kg (25.4%), 1.1 μg/kg (37.8%) and 0.9 μg/kg (24.3%), respectively. Recoveries of the full analytical procedure were 71.7~99.7% for AFB1, 88.1~99.2% for AFB2, 82.8~95.5% for AFG1 and 77.9~90.0%for AFG2. The excess cancer risk estimated using the cancer potency of aflatoxin B1 (7 (mg/kg/day)−1 for HBsAg− and 230 (mg/kg/day)−1 for HBsAg+) were 1.30 × 10^(−5) ~ 1.22 × 10^(−7) for hepatits B surface antigen negative (HBsAg−) and 3.31 × 10^(−4)~ 3.12 × 10^(−6) for hepatits B surface antigen positive (HBsAg+) respectively. In conclusion, although the contamination levels of samples used in the study were low, further actions are also required to undertake a program of herbal surveys in order to access mycotoxin contamination overall so that the safety of public will be protected.