Apaf-1, as a core component of the apoptosoma, is a protein which requires to be strictly regulated. This regulation is evidenced by the growing number of protein partners that have been described, including among others, controversial interactions with members of the Bcl-2 family, heat shock and cell cycle proteins. Furthermore, studies directed to the identification of Apaf-1 chemical modulators is also an emerging field, with promising pharmacological applications in the treatment not only of cancer related diseases but also in degenerative processes. This chapter aims to provide a general view on the actual knowledge related to the cellular regulation of Apaf-1, its protein partners and the latest advances in the identification of chemical modulators.