The rapid detection of Mycobacterium tuberculosis from respiratory specimens is critical for optimal treatment of patients. Several nucleic acid amplification-based systems designed to detect Mycobacterium tuberculosis complex directly from specimens have been developed, and 2 are commercially available. We studied the performance characteristics of these 2 systems (Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD), Gen-Probe, San Diego, Calif; AMPLICOR, Roche Molecular Systems, Branchburg, NJ). Each uses a different amplification strategy, detection modality, and approach to inhibition of amplicon contamination. When compared with culture, the respective sensitivities and specificities were as follows: 92.2% and 98. 7% (study 1) and 88. 7% and 95.3% (study 2); AMPLICOR, 87.5% and 99.7%. Resolution of discordant results was accomplished by incorporating clinical data and multiple specimen analysis. An increased rate of false-positive results was encountered during 1 phase of the study. The conditions under which the test was performed were modified and the "contamination" issue was resolved. This report discusses the benefits and limitations of each assay, proposes cost-effective algorithms for their incorporation into routine laboratory work flow, and discusses the clinical usefulness of these molecular technologies.