The study of gastrointestinal inflammation and repair is key to elucidate the role of different cell populations and molecules during acute and chronic gut inflammatory processes. The proposed collection will function as a group of protocols that will help to disseminate cutting edge techniques in intestinal mucosal inflammation, but also as a guide to define and refine everyday techniques that need standardization. The introduction of veterinary colonoscopes to the field of intestinal mucosal immunology expanded our ability to understand the mechanisms underlying inflammation and repair in vivo. This has inspired researchers to develop innovative approaches to figure out how the responses that drive inflammation and repair occur after an insult compromises the gastrointestinal barrier. In this collection, we will have a compendium of novel techniques that will allow gastrointestinal mucosal immunologists to study the different cell populations and mediators that participate in the inflammatory and repair processes in the gastrointestinal mucosa. We will also include classical but very important techniques that will benefit from standardization in order to make intestinal mucosal research more reproducible among different laboratories. Examples of methods to be found in this collection are murine intestinal loop models to study immune cells trafficking and permeability, immune cell isolation from injured colonic lamina propria, preparation of colonic swiss rolls, and a histological scoring method to standardize murine colitis severity.