Malignant pleural effusion and peritoneal carcinomatosis are frequent causes of effusion. Cytological evaluation (PAP-stained slides followed by immunocytochemistry, IHC, if applicable) is currently the gold standard for the diagnosis of malignant effusions, but its sensitivity varies between 40 and 80%, being a time-consuming technique. Although flow cytometry (FC) is not routinely used in the diagnosis or follow-up of nonhematopoietic neoplasms, it has the advantage of being rapidly applicable to fresh samples, potentially decreasing the time for the diagnosis. The main objective of this study was to assess the utility of FC as a confirmatory tool in the diagnosis of neoplastic effusions, based on the expression of EpCAM antibody in tumor cells versus the cytological evaluation. In this work 1,535 serous fluids were collected, of which 101 (68 pleural, 33 ascites) were selected through a screening algorithm and sent to the FC and cytological evaluation. Seventy-three of these samples (46 pleural, 27 ascites) were considered malignant as determined by clinical, cytological and radiological criteria. According to our data, 75% (55/73) of these samples were positive by Cytology/IHC and 74% (54/73) by FC. We noticed that, although the sensitivity, specificity, and area under the curve were similar, the turnaround time was shorter when using FC. Moreover, these results clearly improved by combining both techniques. We conclude that FC provides information about malignant effusions faster than immunohistochemical staining, and we believe that performing both techniques in parallel would improve diagnostic performance.