A finite element (FE) model of the C5-C6 vertebrae was created and validated with experimental data and then used to investigate the response during the whiplash injury loading condition. The loading condition was defined based on the instantaneous axis of rotation (IAR). The locus of IAR was investigated under the whiplash loading conditions. The stress of lower cervical spine components was investigated in deterministic analysis, and probability of injury was also investigated through the probabilistic analysis. The result showed that the stress was concentrated to the posterior portions in whiplash loading, and it also showed that disc degeneration should be considered as serious whiplash injury factor.