In this study, we tested two rapid molecular methods for the typing of Mycobacterium tuberculosis isolates in the National Tuberculosis Reference Service in Athens, Greece. Randomly amplified polymorphic DNA (RAPD) analysis with three different and/or one arbitrary primers and restriction fragment length polymorphism (RFLP), using non radioactive IS6110 probes, were used comparatively for the molecular typing of the isolates. We found that the PCR-based methods used could successfully type both related and unrelated strains. When the methods were compared for cost effectiveness and simplicity, the RAPD analysis with the IRIS primer was found to be the more convenient to our laboratory. The RAPD methods depend on nonspecific priming and PCR conditions, in a reference laboratory however, we compare strains in the same run and under the same PCR conditions. Pneumon 2000, 13 (2): 102-107