The recent sequencing of the pancreatic cancer genome provides unprecedented insight into the fundamental nature of this deadly malignancy. Although much work still needs to be done, a molecular classification of neoplasms of the pancreas is emerging. Molecular genetics have been used to identify unique clinical subtypes of pancreatic cancer, to guide the clinical diagnosis of pancreatic tumors, and to identify targeted therapies for select pancreatic neoplasms. This review examines the emerging molecular classification of neoplasms of the pancreas. This classification does not ignore previous histology-based classification systems but instead embraces them, creating an integrated histological-molecular classification.