Methods for the rapid diagnosis of infectious diseases have become increasingly common in the last decade. The impetus for the development of such techniques has stemmed from the need to provide clinically relevant information without the length of time and complexity inherent to traditional cultivation methods. This is particularly important in high-risk populations for which more effective antibiotics and antiviral compounds are now available. Assay systems for the immunological detection of microbial agents occupy a central role in the molecular diagnosis of infectious diseases and are rapidly appearing on the market. Novel methods of organism detection by nucleic acid hybridization, long considered usable only in highly specialized laboratories, have the potential for use in routine microbiological laboratories and some systems are now commercially available. As more efficient and rapid diagnostics systems are being developed, the selection of the optimal method will depend on the environment in which the system is to be used. Rapid methods for the detection of infectious agents might markedly improve health care in a variety of clinical, laboratory and epidemiologic situations.