The cytologic examination of fine-needle aspirates and fluid specimens is plagued by a persistent false negative rate. The rate of false negative results will be decreased if sensitive molecular assays can be developed to detect cytologically malignant cells. The current study investigated telomerase expression as a potential marker of malignancy, using the telomeric repeat amplification protocol (TRAP) in fine-needle aspirates and fluid specimens. TRAP was performed on 24 fine-needle aspirate and 24 fluid specimens from different body sites and of different histological diagnoses. We found that 6 of 12 fine-needle aspirate specimens that were cytologically positive for malignant cells expressed telomerase activity, while no specimens that were cytologically suspicious for malignancy, atypical, or negative tested positive for telomerase activity. Of the fluid specimens, 4 of 6 cytologically positive cases and 1 of 18 cytologically negative cases expressed telomerase. Seven of eight telomerase negative, cytologically positive specimens contained only rare malignant cells in a very bloody background. Peripheral blood contamination is a possible pitfall in the TRAP assay, as applied in the current study, because the assay is standardized to protein concentration that may be derived from lysed red blood cells. We conclude that with further technical refinement, the TRAP assay could become a useful adjunct in the cytologic examination of fine-needle aspirates and fluid samples.