The real-time quantitative polymerase chain reaction (PCR), an increasingly popular technique for the detection of DNA, combines a high degree of accuracy with extreme sensitivity. In this chapter we describe the use of real-time quantitative PCR in transplantation research in two areas in which this method is commonly applied: the accurate quantification of mRNA in tissue samples and genotyping of DNA. These are described in the context of cardiac transplantation, but they are of equal relevance to other areas of transplant biology.