Since the discovery of the doublehelix structure of DNA (1), no single event has had the same impact on the field of molecular biology as the rediscovery by Kary Mullis in the early 1980s of the polymerase chain reaction (PCR) (2-4), which was first published in principle by Keld Kleppe in 1971 (5). This elegant technology with its apparent simple theory has revolutionized almost every aspect of classical molecular biology, and is at the present moment beginning to make a major impact upon many medical—especially diagnostic-specialities. The field of clinical microbiology has been among the first to embrace the polymerase chain reaction technology, and the expectations of the future impact of this technology are high. First and foremost, the diagnostic possibilities of this technology are stunning, but in this era of emerging implementation, it is crucial to focus not only on the possibilities, but also on the pitfalls of the technology. Failure to do so will increase the cost of implementation manifold, and will risk to disrepute the technology in the eyes of the clinicians.