Objective: A definitive diagnosis provided by the finding of malignant cells in pleural fluid (PF) can be established in around 50 % of patients with pleural malignancy. However, underdiagnosis risk in cytological suspicious cases is high, which makes the cytological diagnosis quite limited. This is an important clinical problem, especially if we consider that some patients, in bad clinical conditions, can not be submitted to a guided thoracoscopic biopsy. Method: Using multiplex ligation probe-dependent amplification (P315-MRC-Holland) we have studied sequence variations of EGFR gene and amplifications/deletions of chromosomal regions frequently associated to tumors (ATG4B, PAHs, PROS, NSD1, and CDGIF genes). Results: Forty-three malignant PF samples from patients with different cancers were evaluated, even in those cases with scarce pellet cells. Four benign pleural effusions were used as control. Gene sequence changes were observed in 13 (30.2 %) cases, while others copy number abnormalities were found in 19 (44.2 %). Conclusion: The findings suggest that MLPA could be considered an alternative tool to detect molecular genetic changes in malignant pleural effusions, since this technique is relatively low expensive and not time consuming. Our next challenge is to find the best combination of probes capable to recognize malignant cells of any origin in fresh samples of PF.