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Abstract Background Research on diagnosing recurrent non‐small cell lung cancer (NSCLC) and applying target gene treatment using exosomes in a less invasive way is very important. Recently, however, it has been argued that exosomes do not contain double‐stranded DNA (dsDNA) or histones. In this study, we describe the expression of extracellular vesicle (EV) markers in specimens from squamous cell carcinoma (SCC) of the lung and analyze their relationship with the prognosis of patients. Methods Clinical and pathological data were obtained from 96 patients who had undergone surgery for SCC of the lung. Tissue microarray blocks were made using representative paraffin blocks of samples from patients with SCC of the lung. Two pathologists graded the intensity of CD63, CD9, LC3A/B, P62, and ANXA1 expression as high or low expression. In addition, the authors designated the combined expression of these five independent markers as “positive EV expression” in this article. Results SCCs with low CD63 and SCCs with low EV expression showed unfavorable disease‐free survival (DFS) (P‐value = 0.037 and 0.006, respectively) in the survival analysis. The Kaplan‐Meier survival curve confirmed that the low EV expression showed a statistically significant relationship with unfavorable DFS (P‐value = 0.004). There were no statistically significant differences in DFS and disease‐specific survival in each low and high expression group for CD9, LC3A/B, ANXA1, and P62 in the Cox regression analysis. Conclusions As EV expression was related to the prognosis of lung SCC patients, a broader approach using different extracellular vesicles rather than a conventional exosome‐dependent one is needed.