The rapid immunostaining of gastrointestinal cancer-associated antigens, CA19-9, CEA, DUPAN2, and CA50, for intraoperative pathological diagnosis of pancreatic cancer can be completed in only 13 min by applying microwave irradiation, which was used to accelerate the incubation of the primary antibody. Only 3 s irradiation at 500 W for fresh-frozen sections produced specific antigen staining of greater intensity than that obtained with longer incubation, and tissue preservation was satisfactory with minimal non-specific background staining. This rapid immunoperoxidase staining method on the cryostat section of pancreatic biopsy specimens can provide important information for determining an appropriate operative method for pancreatic cancer patients.