BACKGROUNDMalignant pleural effusion (MPE) is a thoracic complication disease characterized by tumors, predominantly resulting from advanced lung cancer. This study aimed to investigate the efficacy of SHOX2 and RASSF1A methylation as a supplementary diagnostic tool for lung cancer-induced MPE with uncertain pathological diagnoses.MATERIALS AND METHODSMethylation-specific polymerase chain reaction (MS-PCR) was used to assess SHOX2 and RASSF1A methylation levels in 98 pleural effusion samples. The cut-off values for SHOX2 and RASSF1A methylation levels for the detection of MPE were determined through receiver operating characteristic (ROC) curve analysis, with corresponding sensitivity and specificity analyses. The chi-square test was used to evaluate the relationship between SHOX2 and RASSF1A methylation levels and clinical characteristics or immunohistochemical markers in patients with MPE.RESULTSFor the diagnosis of MPE, the area under the ROC curve (AUC) values for SHOX2 and RASSF1A methylation levels were 0.820 and 0.718, respectively, with a combined AUC value of 0.881. The sensitivity and specificity of SHOX2 methylation levels were 68.4 % and 92.7 %, respectively, whereas those of RASSF1A methylation levels were 47.4 % and 97.7 %, respectively. The combined detection of SHOX2 and RASSF1A (using the LungMe® assay kit) exhibited a sensitivity of 82.5 %, which exceeded that of cytological analysis (29.8 %). The sensitivity and specificity of combined cytological analysis and LungMe® assay were 89.5 % and 92.7 %, respectively. SHOX2 methylation levels were significantly higher in patients without EGFR mutations than in those with EGFR mutations. The methylation levels of SHOX2 and RASSF1A were higher in smokers than in non-smokers and PDL1-positive patients than in PDL1-negative patients; however, the differences were not statistically significant. The methylation levels of both genes were higher in TTF-1-positive patients than in TTF-1-negative patients, with the difference being statistically significant for RASSF1A.The methylation levels of neither SHOX2 nor RASSF1A were associated with patient survival, whereas PDL1 expression was identified as an independent risk factor for the survival of patients with MPE (hazard ratio = 4.109).CONCLUSIONMethylation of SHOX2 and RASSF1A serves as a valuable diagnostic biomarker for MPE, providing an adjunct to cytological diagnosis.