Objectives: The present study was conducted to determine the prevalence of T-score discordance and its risk factors in a group of patients with spinal cord injury in a university teaching hospital in the Iranian capital of Tehran. Methods: This cross-sectional study was conducted on paraplegic men undergoing bone density testing in an outpatient clinic at a hospital in the Iranian capital, Tehran, between March 2011 and 2012. A questionnaire on demographic and anthropometric characteristics, including age, height, weight, engagement in physical activity and personal smoking habits, was filled out for each subject. All the subjects underwent bone mineral density measurement and blood samples were sent for laboratory testing. Results: Major T-score discordance between two sites was noted in 54 (41.22%) patients. Multivariate logistic regression revealed that every unit increase in serum calcium levels, as the only factor influencing T-score discordance, was associated with a 2.49-fold increased risk in T-score discordance in the area. As for the spine and radius, BMI was the only influencing factor as every unit increase in BMI was associated with a 14% lower risk for T-score discordance in these regions. Body mass index was the only factor, based on the multivariate model, affecting the risk of developing T-score discordance between two sites. Conclusion: Our study revealed the high prevalence of T-score discordance in patients with spinal cord injury. Physicians should therefore be encouraged to perform BMD at three sites when visiting patients with such injuries.