Purpose Mortality in the combined population with incident traumatic spinal cord injury (TSCI) of South Carolina and Colorado is compared to expected five-year mortality. The two states collect similar data on incidence and prevalence of TSCI. These data systems allow population-based estimates of TSCI and provide scientific findings to community partners that bolster advocacy efforts. Methods This retrospective cohort study linked all 1996 and 1997 hospital discharges of incident TSCI cases to the state Multiple Cause of Death Dataset to determine vital status and causes of death by the end of 2002. The National Death Index captured cases that died after establishing residence in other states. Standardized mortality ratios (SMR) were generated for all-cause and specific-cause mortality in the TSCI population relative to the mortality expected in the age-adjusted 1999 U.S. population. Results Five-year mortality after TSCI in the two states was not significantly different. 735 cases of incident TSCI with 103 deaths (14%) were identified in the two states. The majority of cases were uninsured white males 20 to 44 years old. Seventy-five percent of cases were classified as moderate or severe TSCI and 85% occurred with other injuries. The SMR for all-cause mortality was 15.9 (13.0–19.0). Underlying causes of death included vascular disease (SMR 18.3; 12.8–14.4), respiratory disease (SMR 21.6; 10.8–35.0), diabetes (SMR 32.4; 11.8–61.1), and non-TSCI injury (SMR 72.0; 43.3–105.0). Contributing causes of death reported included heart disease (45%), respiratory disease (32%), non-TSCI injury (25%), and diabetes (9%). Conclusion The population discharged from acute care facilities after incident TSCI shows higher incidence of all-cause and specific-cause mortality within 5 years than expected in the general population after adjustment for age.