Background Pancreatico-duodenectomy (PD) is the only potentially curative treatment for pancreatic cancer, but most surgeons are reluctant to perform a palliative resection. The aim was to define the outcome for microscopically incomplete PD (R1). Methods Ninety-nine consecutive patients underwent laparotomy to perform PD. Sixty-seven patients were resected and 32 underwent palliative bypass (PSB) because of locally advanced disease. Results Of the 67 PD, 27 were classified as R0 and 40 as R1. Median survival for R0, R1 and PSB were 24, 18 and 9 months, respectively. Survival in the PSB group was 34% at 1 year and 0% at 2 years. 1-, 2- and 5-year survival in the R0 and R1 groups was 79% and 70%, 48.3% and 39.1%, 21.5% and 9.9%, respectively. Compared to PSB, both other groups were less likely to die over follow-up ( p = 0.002). Survival was not significantly different between the R0 and R1 groups ( p = 0.21). Perioperative morbidity and mortality were similar in the PD and PSB groups (29.9% and 3.0% vs 31.3 and 3.1%, respectively, p = 1.00). Conclusions Better survival in the resection group and similar perioperative risk would support the decision to perform PD even when there is the possibility of incomplete microscopic clearance.