Objective:Genetic assessment of biomarkers in appropriate tumor samples remains to be hallmarks of the real-time individualized therapy in malignant diseases. Malignant effusion is one of the most common presentations in advanced solid cancer. The aim of this study was to characterize cell-free mRNA in malignant effusions and evaluate its association with the sensitivity of primary tumor cells to docetaxel and 5-fluorouracil (5-FU). Methods:Forty-three Malignant effusions samples were prospectively collected from 42 patients. After cell-free RNA extraction and separation of tumor cells,TS and β-tubulin Ⅲ mRNA transcripts in both supernatants and tumor cells were characterized by real-time quantitative PCR. ATP-TCA assay was used to analyze the sensitivity of primary tumor cells to docetaxel and 5-FU. Results:Cell-free TS and β-tubulin IIItranscripts were observed in 42 of 43 specimens. Compared with gene expression patterns in paired-tumor cells,TS mRNA was significantly higher in supernatant whereas β-tubulin Ⅲ mRNA remained the same(P = 0.02). Cell-free TS mRNA was inversely associated with in vitro sensitivity of cancer cells to 5-FU in the gastrointestinal cohort(P = 0.002). Although high β-tubulin III mRNA expression in supernatantsappeared is positively related with cancer cells’ sensitivity to docetaxel,the result didn’t reach the statistical significantce. Conclusion:The cell-free mRNA transcripts in malignant effusions were highly detectable and cell-free TS mRNA levels in gastrointestinal patients were correlated with 5-FU sensitivity.