Cytomegalovirus (CMV) is an important cause of morbidity and mortality in transplant patients, and is typically monitored using laboratory-developed quantitative molecular assays. Clinicians who use quantitative CMV DNA testing should be aware of a number of aspects of testing that will aid in decision making while managing CMV disease in their patients. These include (1) the specimen type used (whole blood or plasma), (2) the limit of detection and limit of quantification chosen by the clinical laboratory, (3) the linear range of the assay, (4) the reproducibility of the assay within the institution, and (5) the wide variability of viral load values among different assays. The biologic properties of CMV, including its variability within the host and of its half-life, are also important factors in the clinical testing for this virus.