Molecular methods for identifying organisms, strain typing, and determining drug susceptibilities are extremely valuable for pathogens that are impossible to grow on artificial media, slow growing on artificial media, or exceptionally hazardous to grow in a clinical microbiology laboratory. DNA hybridization probes and RFLP analysis are currently being used to facilitate the diagnosis and evaluation of mycobacterial disease. PCR is rapidly progressing to the point at which it will become routine in the clinical microbiology laboratory. LCR clearly has a future role in mycobacteriology but requires further understanding of mycobacterial genetics and physiology. The mycobacteriophage reporter-gene assay is an exciting future option that may allow us to obtain critical treatment related information in a much more timely fashion. The technologies mentioned in this article do not include all of the possibilities for the future; however, it can already be imagined that the isolation, identification, and drug-resistance properties of mycobacteria can be determined directly from clinical specimens and the results made available in a matter of days rather than weeks to months. What about the cost? These are expensive methods currently; however, the cost of conventional culture, drug susceptibility determinations, unnecessary periods of isolation for infection control, delays in recognition of resistant isolates, and deaths before the availability of laboratory information are high prices to pay. Only through further investigation can we clarify the most efficient and cost-effective tuberculosis treatment and control program. The dual epidemics of the human immunodeficiency virus and TB will continue to press the scientific community to develop cost-effective approaches, both for developed and developing nations, to a wide array of pathogens. If we do not characterize existing and future organisms at the molecular level, we will be forced to deal with them on their terms and at their leisure.