The purposes of this study was to develop the best one among the methods using dry heat, gamma irradiation and alcohol gas, to sterilize Scutellariae Radix selected based on high frequency of circulation between merchants and high susceptibility to microbial contamination, through comparing these methods in terms of the followings; ⅰ) the efficacy of sterilization in comparison with cost, and ⅱ)the alteration of chemical components of these herbal medicines. The results of this study will be taken advantage of establishment of the maximum limit of microorganism contaminated in herbal medicines. From the results of this study we conclude the followings: ⅰ) The sterilizing method using dry heat may be inappropriate, because it seriously changed their color and morphology which is an essential criterion to estimate a measure of quality between merchants and consumers, although it effectively got rid of contaminated microorganism and did not alter major components, baicalin; ⅱ) The sterilizing method using gamma irradiation may be appropriate, because it showed a strong sterilizing effect, and no alteration of chemical components, color and morphology; ⅲ)The sterilizing method using alcohol gas may also be appropriate, because it had a similar effects as in the case of gamma irradiation. Collectively, we suggest that appropriate sterilizing methods to guarantee the microbial quality of this herbal medicine may be those using gamma irradiation and alcohol gas.