Objective The diagnostic efficacy of the two gene methylation indexes was verified by lung biopsy or postoperative disease examination results.Methods A prospective study was conducted to collect 99 patients diagnosed with pulmonary nodules and masses in the Third People's Hospital of Yunnan Province from March 2019 to March 2020.After bronchoscopy and BALF samples were collected,regular follow-up,lung puncture biopsy and post-operative disease examination were performed.Results Ninety-nine patients with pulmonary nodules and masses were divided into lung cancer group(n = 50)and benign lung disease group(n = 49)after pathological diagnosis.The age of patients in the lung cancer group was(62.64±9.71)years,and that of the benign lung disease group was(60.48±13.69)years,and there was a statistical difference between the two groups(P = 0.032).In the diagnosis of lung cancer,the sensitivity and specificity of SHOX2 and RASSF1A genes alone were found to be 72%and 58%,respectively,and 92.3%and 95.9%,respectively.The combined test of the two genes showed a higher sensitivity in the diagnosis of lung cancer,0.84,compared to 0.102 in the benign disease group(P<0.001).ROC curve analysis showed that the sensitivity of the two genes could be increased to 84%when methylation was combined.Conclusion The methylation test of SHOX2 and RASS1A gene in alveolar lavage fluid has a good value in the diagnosis of lung cancer patients with pulmonary nodules and masses and SHOX2 combined with RASSF1A can be an important supplementary tool for early diagnosis of lung cancer when imaging and histological diagnosis are unclear.