The application of molecular biology to microbiology has led to a. sur
ge of new information about most infectious microorganisms, the pathog
enesis of the infections they cause, and the specific microbial antige
ns involved in the immune response to these infections. The simultaneo
us application of the same techniques to diagnosis and epidemiology ha
s also shown great promise, but these developments have not yet had a
major effect on the routine practice of medicine. For some purposes, d
irect probe tests perform as well as other available methods. However,
for most infections, these methods have not been proven sufficiently
sensitive. The latest generation of highly sensitive diagnostics based
on the polymerase chain reaction will overcome this technical obstacl
e and may revolutionize the management of many infections. Difficultie
s inherent in performing these tests will require special procedures a
nd training in clinical laboratories to ensure that they are performed
reliably. Nucleic acid-based methods for epidemiologic typing of micr
oorganisms and for identification of noncultivatable pathogens are par
ticularly useful for analysis of poorly cultivatable, dangerous, or ot
herwise untypeable microorganisms.