Mesenchymal Stem Cells (MSCs) can both self-renew and differentiate into fat, bone, cartilage, and muscle. They have a high therapeutic value due to their differentiation potential and nonimmunogenic characteristics, however their rareness and duration of their culture are the main handicaps in their application in cell-based therapies. Therefore, our aim was to explore the possible mechanisms that are involved in MSC maintenance and proliferation by using rat MSCs as a model. We studied the effect of estrogen on MSCs due to its role in growth regulation, differentiation, and cellular proliferation. In MSCs isolated from both normal and ovariectomized animals, the number and the CFU activity were increased when cultured with estrogen. To reveal the mechanism of the action of estrogen on MSC maintenance, we investigated the apoptotic pathway since estrogen has been shown to have a detrimental effect on apoptosis in other systems. The number of apoptotic cells decreased when MSCs were cultured in the presence of estrogen. To elucidate the molecular mechanism of estrogen’s effect on MSC apoptosis, we examined the expression of the bcl-2 family of genes. The expression of anti- apoptotic Bcl-2 and Bcl-xL proteins increased in the presence of estrogen, whereas the expression of proapoptotic Bak decreased. Our results clearly show that estrogen increases the number of the functional MSCs by differentially regulating the expression of the bcl-2 family of genes and inhibiting apoptosis. Therefore estrogen treatment of MSCs may offer a potential to increase the number of MSC for treatments.