In effusion cytology, adjuvant techniques are often needed for the differentiation of reactive proliferating mesothelial cells and malignant cells. In the case of malignancy the further challenge is to distinguish metastatic tumors from the primary malignant mesothelioma. Fluorescence in situ hybridization (FISH) of cells in interphase is an accurate method to monitor the genetic status of cells, detecting aneuploid signals and gene deletions. Moreover, it has been proposed that a homozygous deletion of the p16 INK4A gene could more specifically identify malignant mesothelial cells among the exfoliated cells. The first objective of this study was to adapt the commercial FISH-test, UroVysion™ originally designed for the cytological diagnosis of bladder cancer, to the analysis of cells in effusions. The second objective was to test the clinical utility of the test. Sixty-eight pleural effusions were evaluated. The cytological diagnosis was malignant in 29 cases, inconclusive in 24 cases and benign in 15 cases. The independently verified final diagnoses were mesothelioma in 21 cases, metastatic cancer in 29 and benign in 18 cases. The algorithm for aneuploidy distinguished almost all tested malignant conditions from benign ones, also those with inconclusive cytology. The 9p21 locus, carrying the p16 INK4A gene, was homozygously deleted in two of the metastatic cancers, while this was seen in 12 of the 21 malignant mesotheliomas. Thus the commercial UroVysion™-test can be used to accurately distinguish malignant and reactive cells in effusions, particularly when cytology is inconclusive. The test may also indicate presence of MM.