Graft versus host disease (GVHD) is a complication that frequently occurs after haematopoietic stem cell transplantation and concerns many children in paediatric haematology-oncology and bone marrow transplantation departments. It can affect various organs, with the skin, gastrointestinal tract and liver being the most commonly involved. To confirm intestinal GVHD and to rule out differential diagnoses endoscopy is frequently needed. Currently, there are no specific consensus recommendations concerning the best method for endoscopic exploration and medical management of this disease in children, with limited studies available, including a low number of patients. Sigmoidoscopy could be initially proposed under sedation. If sigmoidoscopy is normal or if a general anaesthesia is required, colonoscopy and upper endoscopy should be planned, avoiding duodenal biopsy because of the risk of duodenal haematoma. Regarding therapeutic options, corticosteroids are the first-line treatment for GVHD. Ruxolitinib, a Janus kinase inhibitor, is indicated for children aged 12 years and older with acute or chronic GVHD who have an inadequate response to corticosteroids or other systemic therapies. Nutritional support has a key role in the management of intestinal GVHD and should be considered to guarantee the best possible evolution of intestinal GVHD.