Liquid-based cytology (LBC) is being increasingly used for body fluid specimens and has improved diagnostic accuracy when compared to conventional smears. We compared the diagnostic accuracy and cellular morphologic features between CellprepPlus® LBC and ThinPrep® LBC in effusion cytology. One hundred and eighty body fluid specimens, consisting of 119 pleural fluid specimens, 59 peritoneal fluid specimens, and 2 pericardial fluid specimens, were obtained from 166 patients. Equal volumes of body fluid from each specimen were used in the CellprepPlus® and ThinPrep® preparations. Sensitivity, specificity, and positive and negative predictive values were evaluated. In addition, we selected 16 specimens from patients with metastatic adenocarcinoma, confirmed them by both LBC preparations, and measured the size of the nucleus in the tumor cells in these specimens. The sensitivity of the CellprepPlus® and ThinPrep® methods was 73.1% and 50.0%, respectively. The specificity and positive predictive values were 100% for both LBC methods, and the negative predictive values of the CellprepPlus® and ThinPrep® methods were 90.9% and 83.3%, respectively. The average nuclear size of the tumor cells was calculated as 20.87 μm using the CellprepPlus® method and 15.08 μm using the ThinPrep® method (P < 0.05). The CellprepPlus® method provided better diagnostic accuracy of effusion cytology compared to the ThinPrep® method and revealed the characteristic morphological features of tumor cells, including large and hypochromatic nuclei, prominent nucleoli, distinct nuclear membranes, and high cellularity.