Based on sequence variation in the N-terminus of glycoprotein B (gB), human cytomegalovirus (HCMV) can be classified into four gBn genotypes, and these genotypes are associated with different clinical outcomes. The distribution of gBn genotypes and the level of gBn DNA load were examined in immunocompromised Chinese patients using real-time quantitative PCR. In addition, the PCR and pp65 antigenemia results were compared. In 1480 specimens, 81.4% were antigen-positive, 12.6% were PCR-positive. The gB genotype distribution was as follows among PCR-positive samples: gBn1, 63.1%; gBn2, 13.4%; gBn3, 8.6%; gBn4, not detected; mixed genotypes, 14.9% (gBn1 and gBn3, 14.4%; gBn2 and gBn3, 0.5%). The gBn3 and gBn1 genotypes had the highest and lowest copy numbers, respectively (p<0.05). The quantity of gBn DNA found in PCR-positive, pp65-negative samples was significantly lower than that found in PCR-positive, pp65-positive samples (p<0.05). The PCR and antigenemia results did not differ among bone marrow transplant patients, solid organ transplant patients, and immunocompromised patients without transplantation (p>0.05). HCMV gBn genotyping using real-time quantitative PCR was established successfully, and the distribution of gBn genotypes in immunocompromised Chinese patients was investigated. This method may help to understand better the relationship between gBn genotype and clinical outcome and aid in clinical detection.