This report compares the selective cytotoxic effects of Doenjang fermented by various Bacillus strains (Bacillus sp. SS9, SSA3, and PM3) on human liver cell lines with that of conventional Doenjang (DTY, DTG, and DTK) and commercial Doenjang (DCM, DCD, and DCS). To investigate selective cytotoxic effects of Doenjang extracts, the cell density of HepG2 (Hepatocellular carcinoma) and CCL-13 (cells derived from human normal liver) was estimated after addition of the extracts by using a viable cell counting method. The maximum selectivity ratio ($IC_{50}$value against CCL-13/$IC_{50}$ value aganist HepG2) was observed by PM3 (extracts of Doenjang fermented with Bacillus sp. PM3). As for morphological changes shown by the addition of PM3 into HepG2 and CCL-13 cultures, HepG2 was significantly disrupted, however, CCL-13 was not affected. Also, the growth rate of HepG2 was decreased significantly by the addition of PM3. Consequently, PM3 showed a more detrimental effect on HepG2 than that on CCL-13.