The purpose of this article is to describe specific applications of molecular diagnostics that are currently identifying suspected or unidentified microbial pathogens. The techniques reviewed include (i) the use of specific primers and PCR to identify new microbes, (ii) PCR amplification of conserved 16S rRNA sequence with subsequent identification of specific internal sequence from the candidate bacterial pathogen, and (iii) an exciting new modification of PCR called RDA or "reverse PCR" that can identify unique infectious agents in diseased tissue. The field will continue to expand rapidly and, it is hoped, contribute to a better understanding of the microbial environment with which humans coexist. Also, molecular techniques will eventually be applied in the demonstration of pathogenesis by the various newly identified microbial pathogens.