HACCP methodology was applied in the post-harvest processing and storage of domestic medicinal produces. Particularly in terms of mold and mycotoxin contamination, candidate critical control points (CCP) in the conventional practice in Korean farms were selected and monitored by comparing with on the standard guided processing and storage. When each processing of Angelicae Gigantis Radix were assessed for their safety, the drying steps such as the sun drying or the thermal drying depending on each farm made differences in mold contamination. Moreover, the storage conditions before or after the processing were another critical determinant in the fungal contamination. In other words, storage under 4˚C rather than at room temperature was favorable for reducing mold growth in the harvested crops. Occurrence rate of Aflatoxin B1 (AFB1) in Angelicae Gigantis Radix were 12.8%, but amount of AFB1 in all the collected samples were below 10 ppb regulatory limit allowed in Korea. However, for a few samples of Angelicae Gigantis Radix, still relatively high levels of total amount of the major aflatoxins (aflatoxin B1 + B2 + G1 + G2) were observed around 0.18~49.94 ppb, which is not regulated presently in Korea. It thus can be suggested that post-harvest processing and storage of Korean medicinal crops need further investigation and monitoring to establish the Good Agricultural Practice (GAP), particularly to minimize microbial risk including mold and mycotoxin contamination under the changing climate. Additionally, it is also warranted for new enacting of regulatory limits for total aflatoxins in the medicinal crops.