Background and purpose Pancreatic fistula after pancreatoduodenectomy (PD) is not uncommon, but few reports describe a stricture after pancreatogastrointestinalstomy. We investigated the clinical influence of anastomotic stricture caused by pancreatogastrointestinalstomy after PD. Methods The subjects of this prospective cohort study were 132 patients who underwent PD or pylorus-preserving PD. We reviewed the relationships between pancreatic duct dilatation of the remnant pancreas and several risk factors. We also compared pancreatic duct dilatation with pancreatic atrophy and analyzed nutrient parameters in the first postoperative year. Results Patients with a preoperative pancreatic duct diameter less than 3 mm had a significantly dilated postoperative pancreatic duct diameter (p = 0.0001). The average atrophy rate of the remnant pancreas was 26.3 %, with the lowest atrophy rate (7.3 %) seen in patients without pre- or postoperative pancreatic duct dilation. A normal pancreas in which pancreatic duct dilatation developed postoperatively had a high atrophy rate (34.9 %). Moreover, only patients without pre- or postoperative pancreatic dilatation gained body weight (3.9 %). Conclusions This study shows a significant correlation between pancreatic atrophy rate and weight loss. Atrophy of the remnant pancreas caused by anastomotic stricture influences the exocrine function of patients after PD. The anastomotic method must be improved to prevent pancreatic duct dilatation and allow for early diagnosis and management of stenotic lesions.