Some patients show high serum carcinoembryonic antigen (CEA) levels in the evaluation of candidate patients for lung transplantation, which might be a challenge because high serum CEA potentially implies an existence of malignancy. For further understanding of the true meaning of high serum CEA levels in lung transplantation, we retrospectively investigated the relationship between serum CEA and clinical data. We also performed immunohistochemical analysis of explanted native lungs and evaluated its relationship with serum CEA levels. Retrospective chart review was performed in consecutive patients who underwent lung transplantation with measurement of serum CEA before and after transplantation at our institution between August 2008 and June 2017. Histopathological analysis was also performed in the same cohort of patients. Survival outcomes and pathohistological findings were compared between the high serum CEA and the normal CEA group, adjusting for potential confounding factors. One hundred and fifteen patients were eligible for analysis. High serum CEA levels before lung transplantation in most cases were decreased after the transplantation (35/39, 90%, P < 0.001). Preoperative serum CEA levels were not associated with postoperative survival. The percentage of CEA-positive alveolar cells was significantly higher in the high serum CEA group (P < 0.0001). After adjusting for potential confounding factors, there was a significant difference between the high serum CEA group and normal serum CEA group (CEA-positive alveolar cells; P = 0.002). High serum CEA levels before lung transplantation might derive from native lungs in the recipients and that they were not associated with overall survival after lung transplantation.