**Abstract**

Spinal cord injury (SCI) is a harmful event that involves several repercussions on sensory and motor function that affects the quality of life (QoL) of patients. After SCI, many damage mechanisms are activated that impact on both autonomous extrinsic and intrinsic innervation toward the gut, and these changes modify the gut motility causing bowel dysfunction (BD), an entity that affects 40% of patients with SCI, being the second comorbidity after loss of mobility with no recognized cure. The severity of complications is ruled by the level and severity of injury, having a worse prognosis with an injury that is the most proximal to the brain. In the last 5 years, some experiments have tried to elucidate the consequences of dysbiosis in the gut and aggregated proinflammatory processes. The goal of this chapter is to establish the importance of bacterial composition and immune system repercussions in bowel dysfunction after SCI and how could it give rise to new therapies.

**Keywords:** neurogenic bowel dysfunction, autonomic dysreflexia, gut microbiota, spinal cord injury
