Background: Peptide nucleic acid (PNA)-mediated real-time PCR clamping method is recently introduced to increase the diagnostic sensitivity detecting mutations in various cancers because the diagnostic accuracy of direct sequencing method is not satisfactory in clinical setting. Pleural effusion and serum samples could be easily obtained compared with tumor tissue to examine the mutational status of lung cancer. Methods: 37 NSCLC patients with malignant effusion were enrolled. By using both PNA-mediated real-time PCR clamping method and direct DNA sequencing method, the concordance and diagnostic accuracy of samples from tumor tissue, cell block, pleural effusion and serum were investigated. Results: Ten out of 37 patients (27.0%) and 1 out of 36 patients (2.8%) showed EGFR mutations in pleural effusions and serums, respectively by both PNA-mediated real-time PCR clamping method and direct sequencing method. The overall agree-ment between the two methods were 86% (ĸ coefficient=0.68), 95% (ĸ coefficient=0.91) and 89% (ĸ coefficient=0.75) in tissues, cell blocks and effusions, respectively. The diagnostic accuracy by PNA-mediated real-time PCR clamping method in pleural effusion (sensitivity 0.89, specificity 1.00, positive predictive value 1.00, negative predictive value 0.95) was superior to that of direct sequencing. Conclusion: Although serum samples were not useful to detect EGFR mutational status in lung cancer, pleural effusion samples were comparable with tumor and cell block samples. PNA-mediated real-time PCR clamping method is more sensitive than direct sequencing method to detect EGFR mutation in malignant pleural effusion of lung cancer.