We evaluated a cytomegalovirus (CMV) 24-hour shell vial assay (SVA), the Murex Hybrid Capture CMV DNA assay (HCA), and a CMV plasma PCR for the detection of CMV viremia in renal and bone marrow transplant recipients and human immunodeficiency virus-infected patients. CMV viremia was detected by at least one method in 125 of 317 evaluable samples (39.4%) from 78 patients and was detected in 19.8% of samples by SVA, 26.8% by HCA, and 32.2% by plasma PCR. There was moderate to substantial agreement between the results of the different tests (kappa coefficient = 0.415 to 0.631). However, HCA and plasma PCR were significantly more sensitive than SVA (P = 0.001 and P < 0.0001, respectively; McNemar's test), and plasma PCR was more sensitive than HCA (P = 0.031; McNemar's test). HCA and plasma PCR were more consistently positive than SVA during viremic episodes (P = 0.0002 and P < 0.0001, respectively; McNemar's test). The use of HCA or plasma PCR may therefore improve the diagnosis and management of CMV disease in susceptible patient groups.