Three PCR assays were evaluated for the detection of human cytomegalovirus (HCMV) infection in heart and lung transplant recipients in comparison with HCMV antigenaemia and serology assay. Polymorphonuclear leucocyte (PMNL) samples taken at regular intervals after transplantation were tested for HCMV DNA using primer sets homologous to the glycoprotein B (gp58), major immediate early (IE1), and structural phosphoprotein (pp150) regions. The detection of HCMV infection at various times after transplantation showed all three primer sets to have a sensitivity of 100% and a specificity of 92.3% for the detection of HCMV infection although overall the gp58 primer set was found to be significantly more frequently associated with a positive PCR result than the IE1 (P = 0.0228) and pp150 (P = 0.0015) primer sets. The positive PCR result had a positive predictive value of 27.8% for HCMV disease. Detection of HCMV infection was first by the PCR assay, and significantly before the HCMV antigenaemia assay. Of nine patients who received antiviral therapy while PCR positive, only one patient cleared HCMV DNA from PMNLs during treatment but became positive again 17 days later. Quantitative PCR methodologies may improve the predictive value of PCR for HCMV disease and its value for monitoring antiviral therapy.