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Background: Intrahepatic Biliary Cystadenoma (IBC) is rare but has a high incidence of misdiagnosis, especially for experienceless surgeons. Case: We report a case of IBC located in the caudate lobe and described a typical procedure of misdiagnosing this disease. Finally, the patient was successfully cured, but the procedure of misdiagnosis should attract attention. IBC and atypical biopsy for histological examination are the most important causes of misdiagnosis. Recurrent cystic lesions of the liver and repeated increases in CA 19-9 may suggest a "liver cyst", which is a misdiagnosis. Conclusion: The experience and lessons of misdiagnosis, in this case, may help other clinicians diagnose the rare disease accurately.