Purposes Bowel resection in patients with Crohn’s disease (CD) has a high reported rate of postoperative complications and surgical recurrence. A macroscopically normal resection margin is recommended in CD surgery as wider margins do not translate in reduced recurrence rates. The aim of this study was to evaluate the association between resection margin status and anastomotic complications following ileocaecal resection for primary CD. Methods All patients treated with ileocaecal resection for primary CD from 2010 to 2018 were included in this retrospective observational study. Emergency operations and recurrent CD were excluded. Patients in whom an anastomosis was not fashioned at the time of the surgery were also excluded. Histopathology data collected included macroscopic description, presence of macroscopic and microscopic involvement of the proximal and distal resection margins. The primary outcome was the rate of positive resection margin in patients who developed anastomotic complications (anastomotic leaks and intra-abdominal collections), and the secondary outcomes were overall complications rate, length of hospital stay, reoperations and rehospitalisation within 30 days. Results A total of 104 patients were included. The proximal resection margin was microscopically involved in 19 patients (18.2%). Ten patients (9.6%) developed intra-abdominal anastomotic related complications, with 5 patients out of 10 (50%) in the group of postoperative anastomotic complications having a positive microscopic proximal margin at histology, compared to 14 patients (14.9%) in the group that did not develop anastomotic complications (p < 0.0001). Conclusions Microscopic involvement of the proximal resection margin is more frequent in patients who develop postoperative anastomotic complications following elective ileocaecal resection for primary CD.