Animal models of colitis are widely used to study the pathogenesis of inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). However techniques allowing sequential assessment of colonic inflammation over time, without the need to sacrifice the animal, are required. This study evaluated in vivo colonoscopy to follow the evolution of colitis in rats in comparison with the more commonly used post-mortem macroscopic, microscopic and biochemical assays of inflammation. Colitis was induced in rats by intrarectal instillation of trinitrobenzene sulphonic acid (TNBS).Using a baby upper gastrointestinal endoscope, the severity of colitis was monitored at days 3, 10, 28 and 56 after the induction of colitis. Inflammation was scored by colonoscopy based on the degree of ulceration, extent of inflammation, mucosal bleeding, oedema and stenosis. During follow-up, rats were randomly selected for post-mortem macroscopic and microscopic histology and myeloperoxidase (MPO) assessment of the colon. Colonoscopy showed signs of severe mucosal inflammation in the distal colon 3 days after induction of TNBS colitis. Subsequently, colitis subsided at days 10 and 28 with complete remission at day 56. During the acute phase of inflammation, endoscopic findings were consistent with the post-mortem inflammatory parameters (macroscopic and microscopic histopathology, MPO colonic activity). A strong correlation between endoscopy and macroscopy remained even during the chronic phase of inflammation.