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Context This report describes a minute pancreatic ductal adenocarcinoma which appeared to be in early stage tumor progression based on the study of its molecular abnormalities. In addition, it was associated with lipomatous pseudohypertrophy, a rare disease. Case report A 78-year-old male presented to our department with an incidental pancreatic tumor. Abdominal dynamic computed tomography showed an enlarged pancreas, and diffuse fat density in the entire pancreas was demonstrated. In the pancreatic body, a slightly enhanced early phase 10 mm mass was detected. He underwent a distal pancreatectomy. The histological features of the tumor revealed abundant fibrosis and duct lesions with various atypia. Duct lesions equivalent to well-differentiated adenocarcinoma were shown sparsely, but no vessel or lymphatic permeation nor perineural invasion were observed. In the background of the pancreas, diffuse fatty infiltrations which were composed of abundant normal adipose tissue and scattered pancreatic parenchyma were observed. The results of immunolabeling for MUC1, p16, p53 and Smad4 demonstrated that there is the possibility of coexistence of precancerous duct lesions and cancerous lesions in the genetic progression of pancreatic cancer. Conclusion The above results suggested that this pancreatic ductal adenocarcinoma with lipomatous pseudohypertrophy might be an example of very early stage tumor progression.