The use of nucleic acid amplification techniques within the medical microbiology laboratory is becoming more and more accepted. Polymerase chain reaction (PCR) tests or nucleic acid sequence based amplification (NASBA) assays are already available in the form of commercial kits. Although the technology has been adapted for application in a routine diagnostic setting, some of the systems' characteristics are still amenable to improvement. In this communication several of these aspects will be discussed. Reproducibility of DNA amplification mediated diagnostics and quality control of tests aiming at detection or genetic typing of both viral and bacterial microorganisms, will be discussed. This will be exemplified by the results obtained in multicenter studies on PCR diagnostics of the hepatitis viruses HBV and HCV and by data gathered in the course of PCR mediated DNA fingerprinting of Staphylococcus aureus strains, also performed in different institutes. Application of related techniques such as direct sequencing of amplified (c)DNA or the development of species-specific DNA probes will be described.