Endoscopic mucosectomy is a newly developed endoscopic technique allowing the resection of large fragments of digestive mucosa. The main indications of this technique are the staging and/or the treatment of superficial lesions of esophagus, stomach and colon. Resections by endoscopic mucosectomy raise specific problems of macroscopic technique and histological analysis. For correct inclusion, fragments must be pinned under a rigid support by the endoscopist. Their lateral margins must be sampled independently. The fragment must be included in totality. The histological report must indicate the depth of the resection and its quality, particularly the status of lateral and deep margins. The main difficulties of the histological analysis are due to the frequent occurrence of coagulation artefacts, which may hamper a correct interpretation of the lesions, particularly along the lateral margins. The appropriate management of endoscopic mucosal resections requires a good collaboration between endoscopists and pathologists.