Human cytomegalovirus (HCMV) infection is a common complication in transplant recipients. Sensitive, specific and timely diagnostic tests for the detection of HCMV infection remain essential for successful therapy. The results of three tests to detect HCMV in bone marrow and liver transplant recipients were compared: a pp65 antigenaemia assay, an immediate-early (IE) antigenaemia assay and an anti-HCMV immunoglobulin M (IgM) antibody enzyme-linked immunosorbent assay (ELISA). Of 1344 samples, 911 (67.8%) and 917 (68.2%) samples were positive for pp65 and IE, respectively. The coincidence level was 85.1%. There was no statistical difference after transplantation to the first positive detection of HCMV (mean first checkout time) between the pp65 and IE antigenaemia assays. Moreover, the levels of HCMV detected by the pp65 and IE antigenaemia assays were significantly correlated. The HCMV-positivity rate as detected by the anti-HCMV IgM ELISA was 11.1%, which was significantly different from the IE and pp65 antigenaemia assays. We suggest that the IE antigenaemia assay could replace the pp65 antigenaemia assay for monitoring active HCMV infection and early detection of HCMV infection.