Bak and Bax mediate apoptotic cell death by oligomerizing and forming a pore in the mitochondrial outer membrane. Both proteins anchor to the outer membrane via a C-terminal transmembrane domain, although its topology within the apoptotic pore is not known. Cysteine-scanning mutagenesis and hydrophilic labeling confirmed that in healthy mitochondria the Bak alpha 9 segment traverses the outer membrane, with 11 central residues shielded from labeling. After pore formation those residues remained shielded, indicating that alpha 9 does not line a pore. Bak (and Bax) activation allowed linkage of alpha 9 to neighboring alpha 9 segments, identifying an alpha 9:alpha 9 interface in Bak (and Bax) oligomers. Although the linkage pattern along alpha 9 indicated a preferred packing surface, there was no evidence of a dimerization motif. Rather, the interface was invoked in part by Bak conformation change and in part by BH3:groove dimerization. The alpha 9:alpha 9 interaction may constitute a secondary interface in Bak oligomers, as it could link BH3:groove dimers to high-order oligomers. Moreover, as high-order oligomers were generated when alpha 9:alpha 9 linkage in the membrane was combined with alpha 6:alpha 6 linkage on the membrane surface, the alpha 6-alpha 9 region in oligomerized Bak is flexible. These findings provide the first view of Bak carboxy terminus (C terminus) membrane topology within the apoptotic pore.