For this investigation, 180 samples (20 samples of each Cinnamomi Ramulus, Zingieris Rhizoma, Citri Reticulatae Pericarpium, Oryzae Germinatus Fructus, Coicis Semen, Ginseng Radix, Pinelliae Rhizoma, Moutan Radicis Cortex and Astragali Radix) were collected from Chinese medicinal manufactory plants and drug stores in Taiwan during the fiscal year 2012-2013. In order to investigate the aflatoxin (AF) contamination in Chinese herbs, those samples were analyzed by HPLC according to the 「Method of Test for Mycotoxin in Foods-Test of Aflatoxins」. Aflatoxin was found in 13 samples of Coicis Semen (0.2-56.4 ppb), 11 samples of Oryzae Germinatus Fructus (0.2-10.2 ppb) and 3 sample of Citri Reticulatae Pericarpium (0.1-0.2 ppb). The results can reinforce future guidelines and regulations for regulating authorities.