Patients with spinal cord injury (SCI) often suffer from many gastrointestinal (GI) complaints, while delayed GI transit exists in these patients. We are interested in whether the lost sympathetic activity is one of the mechanisms leading to disturbed GI transit in these subjects. Using a noninvasive hydrogen breath test representing orocecal transit time (OCTT) to study GI transit, 36 SCI patients and 12 age- and sex-matched healthy volunteers were enrolled in our study. Meanwhile, electrocardiogram was performed for all subjects. Finally, spectral analysis of heart rate variability (HRV) was then obtained to assess their sympathovagal balance. SCI patients had higher occurrences of GI symptoms, e.g., nausea/vomiting, belching/hiccup, and constipation, compared to controls (P < 0.05). OCTT was delayed in SCI patients compared to controls (180.8 +/- 10.7 vs 98.3 +/- 14.4 min; P < 0.001). The OCTTs of SCI patients were negatively correlated with their low frequencies of HRV (r = -0.384, P = 0.021). In addition, OCTT was further delayed in quadriplegic patients than paraplegic patients (195.8 +/- 14.5 vs 143.6 +/- 19.4 min; P = 0.031). However, neither the SCI etiology, the injury duration, nor the high frequency of HRV had any influence on the delayed OCTT in SCI patients. We conclude that the GI transit of SCI patients is delayed. This transit disturbance is probably due to loss of sympathetic activity, which is one of the essential components in the coordination of GI peristalsis.