The most cost-effective current use of rapid respiratory virus diagnostics is through highly sensitive and specific molecular assays (mostly PCR-based) in the hospital setting or for chronically ill or immunocompromised outpatients. Specifically, this cost savings is the result of preventing hospitalization or decreasing length of hospitalization, decreasing unnecessary testing and procedures, directing specific therapy, and reducing unnecessary antibiotic use. Equally important is community surveillance by informing physicians rapidly what agents are in the community. Important ongoing issues regarding the cost-effective use of these assays include the cost of reagents or machinery, reimbursement for testing, the need for reliable commercial reagents, the need for open platforms that can respond to new "emerging" or "reemerging" agents, and the need for proficiency panels to share between laboratories. Rapid molecular diagnostic assays for the detection of respiratory viruses have moved into the mainstream of clinical testing. These assays already play important roles in select populations and clinical situations for critical patient management. In addition, there are numerous clinical scenarios where the use of these assays should have a positive cost/benefit ratio. Further work needs to be done to demonstrate this benefit to society. Further development of multiplex assays and decreasing the cost of testing will help improve the benefit of these assays to clinical care. Work is underway on large multiplex molecular assays with high sensitivity and specificity that will be able to be used in an outpatient setting both because of speed and low cost. The future holds great potential for physicians. who soon may be able to answer the age-old question, "Doc, what do I have?" with more than, "You probably have a virus."