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Background: Primary squamous cell carcinoma (SCC) of the pancreas with pseudocysts, especially diagnosed by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA), is extremely rare.Case Presentation: A 64-year-old man was admitted to our department for abdominal distension. Two months ago, he experienced abdominal pain for 1 day and was diagnosed with acute pancreatitis in another hospital. After admission, laboratory tests showed the following: amylase 400 U/L, lipase 403 U/L, and carbohydrate antigen 19-9 (CA19-9) 347 U/mL. Abdominal computed tomography (CT) revealed pancreatitis with a pseudocyst with a diameter measuring 7 cm. During linear EUS, a large pseudocyst (5.4 × 5.2 cm) was observed in the pancreatic body. EUS-FNA was performed. We obtained specimens for histopathology and placed a plastic stent through the pancreas and stomach to drain the pseudocyst. Puncture fluid examination revealed the following: CA19-9 > 12,000 U/mL carcinoembryonic antigen (CEA) 7097.42 ng/ml, amylase 27,145.3 U/L, and lipase > 6000 U/L. Cytopathology revealed an abnormal cell mass, and cancer was suspected. Furthermore, with the result of immunohistochemistry on cell mass (CK ( +), P40 ( +), p63 ( +), CK7 (-) and Ki-67 (30%)), the patient was examined as squamous cell carcinoma (SCC). However, the patient refused surgery, radiotherapy and chemotherapy. After drainage, the cyst shrank, but the patient died 3 months after diagnosis due to liver metastasis and multiple organ failure.Conclusion: For patients with primary pancreatic pseudocysts with elevated serum CEA and CA19-9 levels, we should not rule out pancreatic cancer, which may also be a manifestation of primary pancreatic SCC. EUS-FNA is helpful for obtaining histopathology and cytology and thus improving diagnostic accuracy. [ABSTRACT FROM AUTHOR]