Carbohydrate antigen 19-9 (CA19-9) is widely accepted as a tumor marker for cancers of the biliary, pancreatic and gastrointestinal tracts. Occasionally, CA19-9 is markedly elevated in the serum of patients with benign diseases. Pulmonary sequestration is a rare malformation that is characterized by the presence of lung tissue with abnormal or absent communication with the bronchi, to which blood is supplied by the systemic arteries. The current study. presents a 48-year-old male who presented with upper left abdominal bloating and marked elevation of serum CA19-9 levels. The patient was referred to the Tongji Hospital (Wuhan, China) with suspected hepato-biliary-pancreatic disease and, following surgery, was diagnosed with intralobar pulmonary sequestration. Immunohistochemistry showed marked positive staining for CA19-9 in the sequestrated lung tissue. The patient's symptoms improved and the CA19-9 levels returned to the normal range following surgery. Therefore, the symptoms of upper left abdominal bloating and marked elevation of serum CA19-9 levels, in this case, may have resulted from the intralobar pulmonary sequestration.