Introduction Malignant pleural effusion is a sign of advanced disease with poor prognosis. The function of natural killer (NK) cells is to identify and destroy target tumor cells. This study aims to evaluate the role that cytotoxic NK subpopulations play when diagnosing malignant pleural effusion. Methods NK subpopulations were determined in pleural fluid and peripheral blood by flow cytometry in 71 patients who had suffered pleural effusion of unknown etiology. They were classified into three groups according to their final diagnosis: malignant, paramalignant and benign. Results The NK CD56 dim CD16-subpopulation in peripheral blood was the highest subpopulation in benign than in malignant or paramalignant cases (18.5% vs. 5.5% or 5.6%; p<0.001). Cytotoxic subpopulations NK CD56 dim CD16 + and NK CD16+ were higher in malignant and paramalignant than in benign cases (NK CD56 dim CD16+: 90.7% and 90% vs. 81.4%; p<0.001; NK CD16+: 95% and 95.6% vs. 86.5%; p<0.002). No differences were found in any cells studied in pleural fluid. Conclusions The data from this study suggested that determining the percentage of subpopulations NK CD56 dim CD16+ and NK CD16+, which perform an antibody-dependent cytotoxic function in peripheral blood, can be useful to diagnose malignant pleural effusion.