The lower gastrointestinal system demonstrates significant complexity in its anatomical organization and neural control mechanisms, which are frequently compromised following spinal cord injury. This chapter provides a comprehensive examination of the structural and functional relationships between the lower gastrointestinal tract and its neural control systems, with particular emphasis on the anorectal region and the implications for neurogenic bowel dysfunction after spinal cord injury. The chapter begins by exploring the fundamental architecture of the gastrointestinal wall, including its characteristic four-layered structure and specialized adaptations in the anorectal region. Detailed attention is given to the dual neural control systems: the intrinsic enteric nervous system, which maintains considerable autonomy in regulating basic gut functions, and the extrinsic nervous system, which provides essential modulatory input through sympathetic and parasympathetic pathways. The text progresses to examine the complex innervation patterns of specific gastrointestinal regions, focusing particularly on the unique neural control mechanisms of the rectum and anal canal. The role of various muscle groups, including the internal and external anal sphincters, in maintaining continence and coordinating defecation is extensively discussed. Special consideration is given to the impact of spinal cord injury on these control systems, differentiating between injuries above and below the conus medullaris. The chapter concludes with a detailed analysis of the defecation process, exploring both its voluntary and involuntary components. The intricate coordination between colonic motility, rectal compliance, and sphincter function is examined, along with the various neural pathways involved in maintaining continence and facilitating evacuation. The text highlights how spinal cord injury can disrupt these carefully orchestrated mechanisms, leading to neurogenic bowel dysfunction and associated complications. Throughout the chapter, clinical implications are emphasized, particularly regarding the assessment and management of neurogenic bowel dysfunction following spinal cord injury. Modern diagnostic techniques and their contributions to understanding anorectal physiology are discussed, providing a foundation for evidence-based therapeutic interventions.