Introduction Primary duodenal carcinoma (PDC) is a rare gastrointestinal tumor. The difficult distinction between PDC and other types of carcinoma (e.g. within the periampullary region) is reflected in the scarce literature on true duodenal carcinomas. However, this distinction may be important in relation to the overall prognosis as well as in the choice of adjuvant or palliative treatment strategies. The aim of this study was to evaluate the incidence, management and prognosis of patients with true PDC within a well-defined geographical area. Methods Retrospective analysis of all patients diagnosed with true PDC from 1997 to 2012 within the Region of Southern Denmark. Only patients where the surgeon and the pathologist agreed on the tumor being classified as originating from the duodenum were included. Results Seventy-one patients (43 M, 28 F) with a mean age of 67 years (range 35-87) met the criteria for true PDC. The incidence was 5.4 per 1,000,000, and the pathological classification was: Adenocarcinoma 87%, mucinous adenocarcinoma 7%, carcinoma 4% and signet ring cell carcinoma 1%. Intended curative resection was performed in 28 patients (39%) (22 Whipple procedures and 6 local resections), and all but one patient had negative resection margins. Thirteen patients (46%) had lymph node metastasis. Twenty-nine (67%) of the palliative treated patients had a single (n = 24) or double by-pass procedure (n = 5). The median and 5-year survival for the resected patients were 23 months (CI 7-44) and 27% (CI 10-44). The median survival in the palliative group was 5 months (CI 2-11), and none of the patients were alive after three years. Conclusion The incidence of true PDC within a geographical and histopathologically completely monitored area was 5.4 per 1,000,000. Less than 40% of the patients could be resected and they had a median survival of 23 month and an estimated 5-year survival of 27%. The prognosis of true PDC seemed lower than expected according to previously published data.