Alteration of molecular markers related to apoptosis of in vivo normal system and in vitro cancerous system by soy-isoflavonoid with estrogen was investigated. Down-regulation of Bcl-2 was accompanied by decreased expression of COX-2 (cyclooxygenase-2) in mature female rats treated with soy-isoflavonoid and estrogen. In ovariectomized rat system, Bax was regulated by higher concentration of soy treatment. Bax up-regulation by soy-isoflavonoid genistein treatment was observed in MCF-7 mammary cancer cell system. Estrogen without soy induced similar pattern of Bax expression as soy-isoflavonoid in vivo, but exhibited opposite trend in vitro. These findings suggest soy-isoflavonoid may have potential to induce apoptosis at higher concentrations through up-regulation of Bax or down-regulation of Bcl-2 expressions depending on normal or cancerous state, and physiological status of rats.