Nucleic acid amplification (PCR) allows a relatively rapid and accurate diagnosis of infection caused by intracellular bacteria and other fastidious pathogens for which culture is difficult or impossible. Thus, Chalamydia trachomatis PCR largely improved our ability to diagnose chlamydial infection. PCR also exhibits a high sensitivity and a high reproductibility. However PCR has limitations that have to be taken into consideration to appropriately interpret the results. Such interpretation is difficult and should take into account the characteristics of the test, the microbial agent identified, the sample tested, and the clinical presentation. It is therefore essential that clinical microbiologists and clinicians share their knowledge and expertise to interpret PCR results at both clinical and analytical levels.