In presented study our main aim was to assess the diagnostic yield in submucosal lesions, duodenum wall thickening and surface roughness diagnostics with use of endoscopic ultrasonography. We analysed 41 patients (22 female and 19 male) hospitalized in Military Institute of Medicine in Warsaw between 2009 and 2012 because of duodenum lesion diagnosed in upper gastrointestinal tract endoscopy. In all patients endosonography was performed. In 32 (78.1%) cases organic lesion was diagnosed in gastrointestinal tract wall and in 9 (21.9%) cases normal anatomical structures were found. On the basis of ultrasonography procedure result patients were qualified to surgical, endoscopic or oncology treatment. In 20 (48.8%) cases the change was limited to the mucosa and submucosa and therefore subject to treatment/surveillance endoscopy. In other cases diagnosed infiltration beyond the muscle membrane (n = 21; 51.2%), qualifying of patients for surgery or oncology. Endoscopic ultrasound plays a key role in the diagnosis of submucosal lesions allow proper qualifications to appropriate treatment.