Various mechanical stresses can induce apoptosis of nucleus pulposus (NP) cells and intervertebral disc (IVD) degeneration in vivo, but the underlying molecular mechanism by which the number of NP cells is decreased in degenerated IVD is still not elucidated. The purpose of this study was to investigate whether the mitochondrial pathway is involved in compression-induced apoptosis of rabbit NP cells. The compression apparatus was used to investigate the effect of the compression in this process at one magnitude (1.0 MPa) for 6, 12, 18, 24 and 36 h. Cell viability was measured by cell counting kit-8. Apoptosis rate was analyzed by flow cytometry and the morphologic changes in apoptosis cells were observed by the phase-contrast microscopy and Hoechst 33258 staining. The apoptosis-related gene and protein synthesis, such as Bax, Bcl-2 and Caspase-3, was analyzed by real-time polymerase chain reaction and Western-blot, respectively. Mitochondrial function was evaluated by analyzing the mitochondrial permeability transition pore (MPTP), as well as reactive oxygen species (ROS) and mitochondrial membrane potential (MMP). The results indicated that compression at the magnitude of all time points induced apoptosis of rabbit NP cells in a time-dependent manner, and the cell viability was reduced significantly. Furthermore, the compression at this level profoundly suppressed the functions of the mitochondria such as the opening of MPTP, the excessive production of ROS and the decreased MMP. Our findings suggest that the compression-induced IVD degeneration is mediated, at least in part, via the mitochondrial apoptotic pathway in NP cells.