The exfoliative cell analyzer, LC-1000, is medical device that utilizes the principles of flow cytometry, and might provide digital diagnostic information for cytology using a different approach from conventional cytomorphology. In this study, wae examined the usefulness of the LC-1000 as a diagnostic support system for intraoperative peritoneal lavage cytology and its prognostic impact for pancreatic (PC) and biliary tract cancer (BTC). Patients with PC and BTC who underwent surgical treatment were included. First, we identified useful indicators of LC-1000 and established cutoff values to discriminate positive cytology. Next, we verified the validity of these cutoff values. In the test set (n = 48), of the LC-1000 indicators examined, only MR-CPIx was significantly different between the negative and positive cytology groups, yielding a cutoff value of 0.86. In the validation set (n = 52), the sensitivity, specificity, positive and negative predictive value of the LC-1000 for cytology results was 1.0, 0.49, 0.11 and 1.0, respectively. In patients who had undergone radical resection, recurrence-free survival rate was significantly higher in the LC-1000 negative group than in the positive group in PC, but not in BTC. The LC-1000 was useful as digital support system for peritoneal cytology, and it might have potential as a prognostic factor for PC.