A large amount-260,000 tons-of red paprika is consumed annually in Korea, where the people prefer hot and pungent to sweet foods. Concern has recently grown among consumers over contamination of paprika powder by mycotoxins; contamination can occur at any stage from pre-harvest to drying, storage, grinding, and eventually transport to the retail market. This study had dual aims: to investigate the current level of contamination of hot peppers by ochratoxin A and to identify the critical control points in the food chain. We measured the ochratoxin A (OTA) content of 200 samples from various sources including supermarkets, an online shopping mall, small stakeholder mills, Hazard Analysis and Critical Control Points (HACCP)-implemented factories, and an import company. Mycotoxin was determined using immunoaffinity column cleanup/HPLC quantification as well as strong anion exchange cleanup/stable isotope dilution assay. Monitoring revealed that approximately 30% of red paprika samples were OTA-positive, indicating a need to establish a maximum level for regulation. We selected two model factories that had adopted HACCP in different ways, and compared data in order to develop guidelines for alleviation of mitigation of the mycotoxin contamination.