Efficient detection of recurrent translocation-associated fusion genes is of critical importance for the diagnosis, prognosis and post-therapeutic monitoring of many leukemias. Typically, the presence of such translocations is revealed by RT-PCR technique, followed by Southern blot hybridization to ensure specificity of the PCR product. Though widely employed, post-PCR analysis of this type is relatively laborious and time-intensive. As a departure from standard analytic approaches, we have developed a robust novel method combining both high specificity and sensitivity, based on polystyrene bead capture of fluorescently labeled PCR products, with subsequent analysis by flow cytometry. Results from cell line and patient sample evaluations indicate that this method may be easily incorporated into the diagnostic molecular laboratory as a rapid and cost-effective alternative to currently employed techniques.