The levels of aflatoxin (AFT) and ochratoxin (OCT) were assessed at different seasons in raw materials, different feed manufacture processing stages, and animal feeds in feed mills in Korea implementing the hazard analysis and critical control point (HACCP) system. Two hundred samples were collected in all four seasons from five feed mills implementing the HACCP system and examined for AFT and OCT contents. The AFT and OCT levels were analysed by using HPLC method to provide information on raw material and product stage. The AFT content of raw ingredients in the spring season was highest in corn gluten (3.84 ppb) and lowest in corn (1.82 ppb) The AFT content of corn was highest in the winter season (2.17 ppb). The content of OCT in wheat was highest in the winter season. The amounts of AFT and OCT at processing stages were higher than in the raw materials or feed. In particular, AFT content was higher in the transfer stage (3.88 ppb) than in the mixing (2.86 ppb) or filling stages (3.45 ppb) in the summer season. The means of AFT and OCT level in laying hen feed was 3.41 ppb and 1.14 ppb for broiler feed, respectively. The means of AFT and OCT level in and broiler feeds was 3.44 ppb and 1.17 ppb for broiler feed, respectively.