The cytoplasm and the nucleus have been identified as activity sites for granzyme B (GrB) following its delivery from cytotoxic lymphocyte granules into target cells. Here we report on the ability of exogenous GrB to insert into and function within a proteinase K-resistant mitochondrial compartment. We identified Hax-1 (HS-1-associated protein X-1), a mitochondrial protein involved in the maintenance of mitochondrial membrane potential, as a GrB substrate within the mitochondrion. GrB cleaves Hax-1 into two major fragments: an N-terminal fragment that localizes to mitochondria and a C-terminal fragment that localizes to the cytosol after being released from GrBtreated mitochondria. The N-terminal Hax-1 fragment major cellular impact is on the regulation of mitochondrial polarization. Overexpression of wild-type Hax-1 or its uncleavable mutant form protects the mitochondria against GrB or valinomycin-mediated depolarization. The N-terminal Hax-1 fragment functions as a dominant negative form of Hax-1, mediating mitochondrial depolarization in a cyclophilin D-dependent manner. Thus, induced expression of the N-terminal Hax-1 fragment results in mitochondrial depolarization and subsequent lysosomal degradation of such altered mitochondria. This study is the first to demonstrate GrB activity within the mitochondrion and to identify Hax-1 cleavage as a novel mechanism for GrB-mediated mitochondrial depolarization.The granzyme family of serine proteases are pivotal mediators of apoptosis utilized by cytotoxic lymphocytes against targets such as virus-infected cells and tumor cells (1-6). Granzyme B (GrB) 3 exerts its cytotoxic effect after perforin-dependent intracellular delivery, acting in both cytosolic and nuclear compartments. The capacity of GrB to initiate a mitochondrial apoptotic cascade that features permeabilization of the mitochondrial outer membrane and release of apoptogenic proteins has been tied directly to cleavage of Bid (7-10). GrB-generated tBid activates the downstream executioners of the mitochondrial apoptotic cascade, Bax and/or Bak (11). However, mitochondria of Bid-deficient cells continue to release cytochrome c in response to GrB, suggesting the existence of an alternative mechanism(s). Our recent studies demonstrated that GrB induces a mitochondrial apoptotic cascade by cleaving Mcl-1, an antiapoptotic Bcl-2 family member that resides on the mitochondrial outer membrane in a complex with a potent proapoptotic BH3-only protein, Bim. GrB-mediated degradation of Mcl-1 releases sequestered Bim, allowing the execution of a distinct apoptotic cascade (12, 13). The mitochondrial function of BH3-only proteins, including Bid and Bim, is strictly Bax/Bak-dependent (14). Accordingly, Bax/Bak-deficient cells are relatively resistant to GrB-mediated apoptosis, but mitochondria continue to undergo significant depolarization that cannot be attributed to currently described mechanisms of GrB-mediated apoptosis (10,15,16).Mitochondrial polarization (i.e. maintenance of its inner membrane potential) is ulti...