The Bcl-2 protein family plays a central role in mitochondrial membrane permeabilization. This event and the ensuing release of cytochrome c are decisive in the apoptotic cascade. Therefore, a better knowledge of these processes and their regulation will probably lead to the development of novel therapeutic strategies for the treatment of apoptosis-related diseases. However, the mode of action of Bcl-2 protein family and its regulation are not completely understood. Yeast has proved to be a powerful tool to investigate the molecular aspects of several biological processes, including the steps of the apoptotic cascade involving mitochondria. The fact that yeast does not have obvious homologs of the mammalian Bcl-2 family proteins and that these proteins conserve some of their molecular and biochemical functions when expressed in yeast favor the use of this simpler model system to unravel some of the functions of this family. In this review we attempt to encompass the current knowledge regarding Bcl-2 family mode of action and regulation obtained using the yeast model system. Moreover, we discuss how this model system can be used in the future to gain new understanding about the intricate mechanisms of Bcl-2 family protein regulation, and highlight novel therapeutic targets revealed by this system. We believe that the studies summarized here also provide a proof of principle of yeast as an important tool to elucidate some of the complex mechanisms of apoptotic cell death in higher eukaryotes.