PCR-based diagnosis of infectious diseases has developed into an important method in surgical pathology. We summarize our experience in this area based on 3500 analyses performed during the past 5 years. The peculiarity of material from a pathological laboratory is the risk of DNA fragmentation as a consequence of tissue fixation. For this reason the assays used must be adapted to this particular situation. PCR-based diagnosis of infectious diseases, if performed according to appropriate quality standards, is a safe and effective technique with high sensitivity and specificity and results in an etiologically based diagnosis.