The purpose of this study was to develop the best methods to sterilize herbal medicines which is frequently used and known to have high susceptibility to microbial contamination. We used dry heat, gamma irradiation and alcohol gas treatment for sterilization, and evaluated these methods in terms of the followings; i) the efficacy of sterilization, and ii) the chemical alteration of index constituents of herbal medicines. Treatment with dry heat effectively eliminated the contaminated microorganisms, and did not significantly alter the content of berberine chloride, paeoniflorin and amygdalin in Phellodendron Bark, Peony Root and Apricot Kernel, respectively: However it seriously changed the color and morphology which are essential criteria to estimate a measure of quality of herbal medicines. Treatment with gamma irradiation showed a strong sterilizing effect, and no alteration of the content of index constituents, color and morphology: Alcohol gas treatment resulted in similar effects as those in gamma irradiation. Collectively; these results suggest that treatment with gamma irradiation or alcohol gas may be useful methods for sterilizing herbal medicines without a decrease in their microbial quality.