Endoscopic ultrasound guided fine-needle aspiration biopsy is a reliable and accurate method for the diagnosis of submucosal lesions of the gastrointestinal tract. We report the cytopathologic findings of a case of duodenal high-grade neuroendocrine carcinoma in a 68-year-old woman who presented with melena and marked anemia, 45 years after kidney transplantation. Imaging studies performed in the work-up of melena showed a duodenal mass, which on endoscopy proved to be an exophytic, villous duodenal lesion, 3 cm from the ampulla. Forceps biopsy of the exophytic lesion showed a villous adenoma. Endoscopic ultrasound additionally revealed an underlying submucosal lesion and EUS-guided fine needle aspiration of this submucosal mass and of the enlarged mesenteric lymph nodes was diagnostic of a high-grade neuroendocrine carcinoma. The aspirates showed abundant cellularity with tumor cells arranged in sheets and occasional loose clusters. The neoplastic cells had a moderate amount of pale cytoplasm and large round to oval hyperchromatic nuclei with focally prominent nucleoli. Mitoses, apoptotic bodies and necrotic debris were also present. The tumor cells were strongly and diffusely positive for cytokeratin AE1/AE3, synaptophysin and chromogranin and showed a very high proliferative fraction on Ki67 staining, supporting the diagnosis of a high-grade neuroendocrine carcinoma. This is to our knowledge the first case of high-grade neuroendocrine carcinoma of the duodenum diagnosed by EUS-FNA. This case also emphasizes the diagnostic value of EUS-FNA sampling of the submucosal and intramural component of villous tumors of the gastrointestinal tract when mucosal forceps biopsies show only benign findings. Diagn. Cytopathol. 2012. © 2010 Wiley Periodicals, Inc.