Objective: The cytological diagnosis of coelomic fluid is essential for examining malignant mesothelioma (MM). However, reactive mesothelium (RM), caused by various factors, is morphologically similar to MM and thus often complicates the differential diagnosis. Here, nuclear luminance and steric alterations were assessed for the discriminant analysis of MM and RM. Study Design: Thirteen epithelial MM and 11 RM cases were included. One hundred alterations in the numbers of nuclear pixels and focus layers and the coefficient of variation of nuclear luminance among layers were determined for each case to conduct discriminant analysis using the Mahalanobis distance. Results: A cutoff value of 0.072 allowed highly accurate discrimination of MM (89.5%) and RM (89.6%). Fifteen cells appeared in 6 agglomerates of indiscriminable MM cases. The 6 agglomerates were individually examined. Malignant cells were dominant in 3 agglomerates (50%), allowing the discrimination of malignant cases. Conclusion: Discrimination using nuclear luminance and steric alterations is useful for morphologically indiscriminable MM cases. Three-dimensional analysis of agglomerates will be further investigated to improve the diagnostic accuracy.