BACKGROUND: Little information is available concerning the biomechanism involved in the spinal cord injury after cervical rotatory manipulation (CRM). The primary purpose of this study was to explore the biomechanical and kinematic effects of CRM on a healthy spinal cord. METHODS: A finite element (FE) model of the basilaris cranii, C1-C7 vertebral bodies, nerve root complex and vertebral canal contents was constructed and validated against in vivo and in vitro published data. The FE model simulated CRM in the flexion, extension and neutral positions. The stress distribution, forma and relative position of the spinal cord were observed. RESULTS: Lower von Mises stress was observed on the spinal cord after CRM in the flexion position. The spinal cord in CRM in the flexion and neutral positions had a lower sagittal diameter and cross-sectional area. In addition, the spinal cord was anteriorly positioned after CRM in the flexion position, while the spinal cord was posteriorly positioned after CRM in the extension and neutral positions. CONCLUSION: CRM in the flexion position is less likely to injure the spinal cord, but caution is warranted when posterior vertebral osteophytes or disc herniations exist.