Broad range 16S rDNA PCR can be used to facilitate the diagnosis of infectious diseases of bacterial origin by detecting 16S rDNA sequences in patient samples. Post amplification sequencing facilitates identification of the infecting organism, but may not allow for differentiation at the species or strain level. This review focuses on the historical use and current applications of broad range 16S rDNA PCR in the diagnosis of bacterial infection. Use of an enrichment liquid culture prior to PCR and the use of real time PCR are also considered. A review of the literature indicates that the diagnostic utility of broad range 16S rDNA PCR is enhanced substantially, if the detected organism is a well-documented pathogen. Frequent detection of environmental organisms of undetermined pathogenicity is currently a limitation. This review also examines weighted criteria developed by different researchers and proposes a decision making tree that establishes the relative importance of various criteria for attributing diagnostic relevance when evaluating individual patient samples. Based upon our review of the literature, a more uniform consensus on the accurate interpretation of broad range 16S rDNA PCR results are needed to improve the microbiological utility of this modality for the diagnosis of bacterial infections in animals and in human patients.