In the very beginning of polymerase chain reaction (PCR) tests entering the field of diagnosis of infectious agents, the introduction of this technology into routine diagnosis was hampered by its frequent tendency to create false-positive results because of contamination. This problem is now widely solved by the introduction of the uracil-N-glycosylase (UNG) anticontamination technology. However, care must still be taken to avoid other sources of producing false positive results. They might additionally derive from human error and/or insufficient PCR amplification and detection protocols. A special case lies in the fact that PCR also amplifies DNA from dead organisms rendering a result diagnostically correct as positive, but clinically as false-positive. In PCR, as in any other diagnostic test, the risk of creating a false-negative result also exists. In such a case, the most probable source besides human error, low target or poor amplification and detection protocols is an inhibition caused by interfering substances in a patient's sample. Strategies to recognize and overcome this issue are discussed in this article. Finally a few results from quality control studies on amplification technologies in the diagnosis of infectious agents are reviewed.