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A molecular analysis of pancreatic cyst fluid is revolutionizing the clinical management of pancreatic cysts. Yet, there remains need for ongoing correlation of molecular testing with surgical pathology. An ~70-year old male was found to have focal main pancreatic duct dilation up to 7 mm at the pancreatic head/neck on imaging without any discrete mass lesions. Duct fluid analysis found elevated carcinoembryonic antigen and decreased glucose level suggestive of intraductal papillary mucinous neoplasm (IPMN). Yet, molecular testing revealed no mutations. In the absence of a mass lesion, he was recommended surveillance. A year later, he had stable imaging and underwent repeat molecular testing, which revealed KRAS and GNAS mutations. He underwent pancreatoduodenectomy for suspected main duct IPMN. Final pathology revealed low-grade, multifocal pancreatic intraepithelial neoplasia, not IPMN. Ongoing assessment of concordance between molecular testing and postoperative pathology after pancreatectomy is needed to refine the multimodal diagnostic evaluation of pancreatic cysts.