Background Neuroendocrine tumors (NET) account for one-third of all small bowel neoplasms. The search for the primary tumor in NET is important, even though it is difficult to localize, as its surgical excision leads to a better prognosis, even in metastasized stages of the disease. The objective of this study was to evaluate the use of double balloon enteroscopy (DBE) for the detection of the primary tumor in patients with NET. Methods Twelve consecutive patients (eight women, four men) with suspected carcinoid syndrome, either metastatic to the liver (n = 5), symptoms of a neuroendocrine tumor with elevated tumor markers (n = 5), or obscure gastrointestinal bleeding (n = 2) underwent DBE for the search of the primary tumor or the source of bleeding. All patients underwent abdominal sonography and a computed tomography (CT) scan, esophagogastroduodenoscopy (EGD), ileocolonoscopy, and octreotide scintigraphy prior to DBE. Capsule endoscopy was performed in four patients. Results A total of 17 DBE were performed in the 12 patients. The CT scan and sonography of the abdomen as well as EGD and ileocolonoscopy were unable to detect the primary tumor in any patient. A submucosal tumor of the ileum or the jejunum could be detected by DBE was detected in seven patients (58%) (anal route, n = 4; oral route, n = 3). In four of these patients (33%) this finding could be confirmed by the surgical resection of a NET. In two patients (17%) with a submucosal ileum protrusion suspicious for NET, laparotomy and intraoperative endoscopy did not confirm the tumor. Conclusions In this study, the diagnostic yield of DBE for primary tumor search in patients with metastatic or suspected NET was 33%. Although endoscopic small bowel investigation by DBE seems to enrich the diagnostic possibilities for the diagnosis of small bowel-NET, at the present time DBE should only be performed in selected cases, possibly based on a positive previous work-up.