Methods: A total of 51 patients with a mean age of 31.75±10.42 years who suffered traumatic SCI were included in this study. Complete neurological examinations (American Spinal Injury Association grading) and magnetic resonance imaging (MRI) were performed at the time of admission and at 3–6 months after injury to study the neurological status and disc and trunk parameters. The type of management (operative or conservative) was decided on the basis of clinical, radiological, and MRI evaluations, and a robust rehabilitation program was initiated. Results: Disc parameters including disc angle, skin angle, cross-sectional area (CSA), and disc height and trunk parameters (mean trunk width, mean trunk depth, and CSA of the lumbar muscles) decreased significantly (p <0.001) during the first 3 months after SCI. However, improvements were observed in disc and muscle parameters at the 6-month follow-up, but these parameters did not return to normal levels. Neither initial neurological status (complete vs. incomplete) nor type of management (operative vs. conservative) had a significant effect on these parameters. Conclusions Spinal trauma leads to alterations in the morphology of the vertebral column, spinal cord, intervertebral discs, and paraspinal muscles in the initial phase of injury. The extent of these changes may determine the initial neurological deficit and subsequent recovery. Although this study did not identify any statistically significant effect of neurological status or management strategy on these parameters, rehabilitation was found to result in the improvement of these parameters in the later phase of recovery. Future studies are required to evaluate the exact causes of these alterations and the potential benefits of rehabilitation strategies and to minimize these changes.