The amplification of nucleic acids is often used for the diagnosis and the follow-up of infectious diseases. The interpretation of PCR results varies according to the pathogens detected, the site of infection and the clinical presentation. PCR tests might be the reference method or only an help for the diagnosis. With the development of antiviral treatments quantitative PCR tests are now essential for the evaluation of treatment efficacy. A discussion with the laboratory is important for the correct interpretation of PCR results.