Objective: Patients with spinal cord injury and disorder (SCI/D) have an increased risk of infection with multidrug-resistant (MDR) bacteria. We described bacterial epidemiology and resistance in patients with SCI/D at Veterans Affairs Medical Centers (VAMCs) for the past 9 years.Design: Retrospective cohort.Setting: One hundred thirty VAMCs.Participants: Veterans with SCI/D and bacterial cultures with antibiotic susceptibility testing performed between 1/1/2005–12/31/2013. Single cultures with contaminants and duplicate isolates within 30 days of initial isolates were excluded.Interventions: None.Outcomes: Trends in microbial epidemiology and antibiotic resistance.Results: Included were 216,504 isolates from 19,421 patients. Urine was the most common source and Gram-negative bacteria (GNB) were isolated most often, with 36.1% of GNB being MDR. Logistic regression models clustered by patient and adjusted for location at an SCI/D center and geographic region showed increased odds over time of vancomycin resistance in Enterococcus [adjusted odds ratio (aOR) 1.67, 95% confidence interval (CI) 1.30–2.15], while methicillin resistance in Staphylococcus aureus remained unchanged (aOR 0.90, 95% CI 0.74–1.09). There were also increased odds of fluoroquinolone resistance (aOR 1.39, 95% CI 1.31–1.47) and multidrug resistance (aOR 1.46, 95% CI 1.38–1.55) in GNB, with variability in the odds of MDR bacteria by geographic region.Conclusions: GNB are isolated frequently in Veterans with SCI/D and have demonstrated increasing resistance over the past 9 years. Priority should be given to controlling the spread of resistant bacteria in this population. Knowledge of local and regional epidemiologic trends in antibiotic resistance in patients with SCI/D may improve appropriate antibiotic prescribing.