The peripheral benzodiazepine receptor (PBR) is a component of a multiprotein complex, located at the contact site between the inner and outer mitochondrial membranes, which constitutes the mitochondrial permeability transition (MPT)-pore. The opening of the MPT-pore, leading to the transmembrane mitochondrial potential (ΔΨm) dissipation, is a critical event in the mechanism of apoptosis. In the present work, we investigated the ability of the specific PBR ligands, PK 11195 or Ro5-4864, to affect mitochondrial potential and to induce apoptotic cell death in rat C6 glioma cells. Both specific ligands inhibited cell survival in a dose- and time-dependent manner, as assessed by MTS conversion assay, whereas the non-site selective ligand Diazepam or the low-affinity benzodiazepine Clonazepam showed no significant effects. After cell exposure to PK 11195 or Ro5-4864 we evidenced typical alterations of apoptotic cell death such as DNA fragmentation and chromatin condensation assessed by flow cytometric and transmission electron microscopy (TEM) analysis, respectively. Activation of the “effector” caspase-3 confirmed the ability of specific PBR ligands to induce apoptosis. Moreover, PK 11195 and Ro5-4864 induced a decrease of ΔΨm, as evidenced by JC-1 flow cytometry analysis. Our data demonstrate the pro-apoptotic effects of specific PBR ligands on rat C6 glioma cells.