To find anti-apoptotic substances in plant resources, a microassay method for estimating DNA fragmentation was established using fluorochrome 3,5-diaminobenzoic acid dihydrochloride. Examination was made of various herbal medicines for inhibitory effects on glucocorticoid-induced apoptosis in thymocytes. Several Kampo medicines, e.g. Oren-gedoku-to and San'o-shashin-to, were found to inhibit dexamethasone-induced apoptosis in murine thymocytes. Some of these medicines contain Coptidis rhizoma (CR) as the major constituent, and the CR extract showed the most potent inhibitory activity on thymocyte apoptosis of more than 200 species of herbal extracts. The inhibition of apoptosis by CR extract was confirmed by the trypan blue exclusion test, lactate dehydrogenase release measurement, and morphological evaluation by electron microscopy. The benzodioxolo-benzoquinolizine alkaloid, berberine, and five berberine-type alkaloids, isolated from CR extract, had an inhibitory effect, whereas no effect was noted for the aporphin-type alkaloid magnoflorine. The inhibitory action of berberine was also demonstrated on etoposide- and camptothecin-induced apoptosis.