Human cytomegalovirus (HCMV) genomic polymorphisms have been used to investigate correlations between virus variants and clinical characteristics. We explored the distribution of HCMV glycoprotein N (gN) genotypes and their roles relative to clinical features in a population of Chinese hematopoietic stem cell transplant (HSCT) recipients. This prospective analysis involved HCMV clinical isolates obtained from 102 HSCT patients. Real-time quantitative PCR and PCR-based restriction fragment length polymorphism analysis were applied for the determination of viral loads and gN genotypes. The distribution of HCMV gN genotypes was as follows: gN1, 6/102 (5.9%); gN2, 10/102 (9.8%); gN3a, 17/102 (16.7%); gN3b, 5/102 (4.9%); gN4a, 12/102 (11.7%); gN4b, 9/102 (8.8%); gN4d, 2/102 (2.0%); and mixtures, 41/102 (40.2%). No particular HCMV gN genotype was significantly associated with specific clinical characteristics. The HCMV gN3a genotype was the most prevalent among Chinese HSCT recipients, but HCMV gN genotypes may have no correlation with clinical features in HSCT patients.