Complex biological structures involve uncertain parameters that may produce unexpected responses in the structures. The cervical spine is one of the most complex structures in human body. It is essential to consider the uncertainties contained in the cervical spine for accurate injury analysis. For this research, a finite element (FE) model of cervical spine column is created based on medical images. The FE model involves the skull, the vertebral body (C1-T1), the disc between adjacent vertebral bodies, and the ligaments. The disc consists of the annulus, nucleus, and fiber. The material property and disc height are adjusted for the disc degeneration levels in FE analysis. The FE model is validated with the experimental data. Probabilistic FE analysis is used to account for uncertainties of cervical spine components. Material properties of the disc are considered as random variables, which are defined by means, standard deviations, and distributions. In this study, the probability of injury of the disc, under dynamic loading, is investigated at various disc degeneration levels under dynamic loads. The result shows that the probability of injury was drastically increased with the disc degeneration levels. Even if the disc fracture was not reported and the magnitude of stress was small in whiplash loading, the possibility of disc injuries is increased when a degenerated disc was exposed to whiplash loading. The results presented in this research make a contribution to the understanding of age-related whiplash injuries. The results also provide evidence that the reliability of biomechanical injury analysis is also increased by accounting for uncertain factors contained in biological structures.