In the initiation of apoptosis, the Bcl-2 family members Bax and Bak play the pivotal role of impairing mitochondrial integrity, by oligomerising in the outer mitochondrial membrane and forming pores in it. However, how certain ligands activate these proteins and the nature of the conformational changes leading to oligomer formation remain poorly understood. To clarify these critical steps, which have been termed the “Holy Grail” of apoptosis research, we have employed both structural and biochemical approaches. A simple in vitro assay for Bax activation by detergents and activating ligands has allowed us to capture an early Bax transition and to determine the first ever crystal structure of a Bax:ligand complex. The structure not only revealed the binding site on Bax and allowed identification of residues crucial for the interaction but also disclosed unexpected ligand-induced conformation changes in Bax that trigger its oligomerisation. In addition, we have studied Bak conformation changes on mitochondrial membranes of mammalian cells using a cysteine-substitution and -labelling assay that monitors the degree of burial of Bak domains within hydrophobic environments. This approach has yielded insights into the general structure of the inactive Bak monomer, transient conformational changes during its activation and the membrane-topology of the Bak oligomer. The results we have obtained challenge prevailing views about how Bax and Bak become activated for death duty and oligomerise in the mitochondrial outer membrane.