Objective: To establish a method to determine aflatoxins B1

B2

G1

G2 in Chinese Materia Medica and pharmaceutical intermediates microbiological contaminated by immunoaffinity column clean-up combined with post-column derivatization and HPLC-FD detection. Method: Using immunoaffinity column clean-up combined with post-column derivatization

the analytical method to detect aflatoxins B1

B2

G1

G2 was established firstly

and then 14 kind of Chinese Materia Medica and pharmaceutical intermediates microbiological contaminated was detected respectively. Result: The method with the great linear concentration range of 0.15-6.0 ng·mL-1 for aflatoxins G2

B2

and 0.5-20.0 μg·L-1for G1

B1 respectively

was stable and accurate. As a result

aflatoxins B1was detected in Chuanxiong Rhizoma and Platycladi Semen in the 14 kind of Chinese Materia Medica

while there were none of aflatoxins in the pharmaceutical intermediates made by Chuanxiong Rhizoma. Conclusion: The method established in this study was specific and accurate for the detection of aflatoxins in Chinese Materia Medica and pharmaceutical intermediates.