The gastrointestinal tract is a unique organ system that provides an epithelial barrier between our underlying immune system and luminal pathogens. Disruption of gastrointestinal homeostasis, as a result of impaired barrier function, is associated with numerous pathologies including inflammatory bowel disease and colorectal cancer. In parallel to the clinical development of endoscopy technologies to monitor and diagnose these pathologies in humans, advanced mouse colonoscopy techniques are being developed. When these technologies are coupled with model systems of human disease, which are essential to our understanding of the pathophysiology of gastrointestinal diseases, the requirement for euthanasia of multiple cohorts of mice is eliminated. Here we highlight the suitability of white light endoscopy to monitor the progression of colitis in mice. We further outline the experimental power of combined standard endoscopy with confocal microendoscopy, which permits visualization of fluorescent markers in a single animal in real-time. Together, these technologies will enhance our understanding of the interplay between components of the gastrointestinal microenvironment and their role in disease.