Background: Gastrointestinal dysfunction and vein thrombosis are well-known acute complications after spinal cord injuries (SCIs). Objective: To determine the frequency and risk factors for deep vein thrombosis (DVT) and small-intestinal bacterial overgrowth (SIBO) in patients with SCI. Methods: A total of 377 consecutive eligible SCI patients tested for SIBO with the glucose hydrogen/methane breath test from January 2011 to December 2015 and who had also undergone venous ultrasound study for suspected DVT were evaluated within 3 months after admission. Results: Seventy-six of the 377 SCI patients were DVT-positive (20.2%; 95% confidence interval [CI] 16.1-24.2%), and 145 were SIBOpositive (38.5%; 95% CI 29.9-59.0%). Among the 76 DVT-positive patients, 60 were SIBO-positive and 16 were SIBO-negative. The difference was statistically significant (41.4% versus 6.9%; odds ratio [OR] 5.99; 95% CI 3.15-9.33). Among the 145 SIBO-positive patients, 60 were DVT-positive and 85 were DVT-negative. The difference was statistically significant (78.9% versus 28.2%; OR 2.88; 95% CI 2.12-4.47). In the stepwise multivariate logistic regression, a family history of venous thrombosis (OR 2.32; 95% CI 1.60-3.79), chronic kidney disease (OR 2.99; 95% CI 1.73-5.08) and the presence of SIBO (OR 3.72; 95% CI 1.97-6.62) remained associated with DVT. Conclusions: These data support an association between SIBO and DVT in SCI patients. Further studies should be carried out with respect to the relationship between SIBO and DVT.