The differential diagnosis between malignancy-related and non-malignant pericardial effusions has remained an essential problem in clinical practise. Cytologic examination is considered as gold standard with an average specificity being close to 100 % but still this is not disclaiming the possibility of false positive results. Hence our principal goal was to evaluate the usefulness of the detection of telomerase activity in pericardial effusions to gain another indicator for the presence of tumour cells in effusions. 31 pericardial fluid samples were collected from consecutive, unselected patients undergoing a therapeutic or diagnostic pericardiocentesis. Measurement of telomerase activity was performed with a conventional isotopic and a fluorescence-based TRAP assay (Telomeric Repeat Amplification Protocol). The results of the isotopic TRAP assay indicate a strong correlation between elevated telomerase activity and cytopathologically confirmed presence of malignant cells in pericardial effusions: the sensitivity was 100 % and the specificity was 91,7 %. As low levels of telomerase activity can also be detected in stem cells and hematopoietic progenitor cells false-positive results may occur. For this reason we established a fluorescence based F-TRAP assay allowing the quantitative analysis of telomerase activity. The origin of the telomerase activity should be specified by the quantification.Therefore the fluorescence based assay was calibrated by a dilution standard containing human small cell lung cancer cells (NCI-H69) known to be telomerase-positive. In addition we checked possible background telomerase activity in pericardial effusions by assaying CD34-positive cells and monocytes from peripheral blood. Telomerase activity was detected in low levels in both cell types. A cut-off value for background activity could be determined enabling the discrimination between benign inflammatory and malignant tumour cells. The cut-off value also provided a further increase in specificity up to 95,8 % without a loss of sensitivity. We noticed a relative good quality of extracts obtained allowing a reliable analysis and presume that pericardial effusions may be especially rewarding because of the low presence of RNAses and proteinases secreted by surrounding cells. The results of both TRAP assays indicate that the determination of telomerase activity is a reliable indicator for the presence of tumour cells in pericardial effusions and is therefore a useful adjunctive diagnostic tool for cytological and clinicopathological diagnosis.