Quantitative monitoring of human cytomegalovirus (HCMV) infections is helpful in determining appropriate antiviral management of bone marrow transplant (BMT) recipients. The objective of this study was to design and evaluate a new HCMV capture-hybrid PCR-ELISA in plasma and peripheral blood mononuclear cells (PBMCs) to monitor HCMV infection in a population of bone marrow transplant recipients. Twenty six allogeneic bone marrow transplant recipients, including 17 males and 9 females (9 adults and 17 children), were enrolled in this study. A total of 313 consecutive whole-blood specimens from 0 to 120 days post-transplantation were evaluated in the study. A newly design biotinylated probe mediated quantitative competitive PCR-ELISA test was used to determine HCMV viral load in samples. All 26 patients were HCMV sero-positive before transplantation. Capture-hybrid PCR-ELISA of PBMCs detected HCMV DNA in 287 of 313 specimens, also PCR-ELISA of plasma detected HCMV nucleic acid in 114 of 313 specimens. Increasing titers of HCMV DNA were detected in 14 of 26 BMT recipients. In conclusion, the developed quantitative capture-hybrid PCR-ELISA demonstrated the capability of monitoring and diagnosis of HCMV infection in bone marrow transplant recipients. Although PCR-ELISA detection of DNA in PBMCs was the earliest and most sensitive technique used for the diagnosis of HCMV nucleic acid, but PCR on plasma was more predictive of the onset of HCMV-related clinical symptoms.