The objective of this study was to investigate the occurrence of aflatoxins in herbal medicines distributed in South Korea. A total of 700 herbal medicine samples (10 samples each for 70 types of herbal medicine) were analyzed by an enzyme-linked immunosorbent assay (ELISA) for aflatoxin B(1) (AFB(1)), and levels of total aflatoxins were quantified and confirmed by liquid chromatography combined with tandem mass spectrometry (LC-MS/MS). The levels of recovery of the methods were 84.30 to 102.68% (ELISA for AFB(1)) and 72.17 to 90.92% (LC-MS/MS for total aflatoxins). Fifty-eight (8.29%) of 700 samples were AFB(1) positive by ELISA, and 17 (2.43%) of them were finally confirmed as positive for total aflatoxins by LC-MS/MS. Total aflatoxin levels in the herbal medicines were from 4.51 to 108.42 μg/kg. Among the 17 samples, the AFB(1) content of 6 samples (11.95 to 73.27 μg/kg) and the total aflatoxin content of 10 (12.12 to 108.42 μg/kg) samples exceeded the legal limits set by the Korea Food and Drug Administration for AFB(1) (10 μg/kg) and by the European Commission for total aflatoxins (10 μg/kg), respectively. These results demonstrate the risk to consumers of herbal medicine contamination by aflatoxins and encourage further studies to investigate the transfer rate of mycotoxins to decoction, which is the final product for consumption.