Objective To analyze the distribution of various genotypes of human cytomegalovirus glycoprotein N (HCMV gN) in patients with HIV infection; to investigate the effects of HCMV-HIV co-infection on disease progression and the relationships between HCMV gN genotypes and disease progression. Methods Patients with active HCMV infection were screened out from 359 patients with HIV infection by using the pp65 antigenemia assay. The genes encoding HCMV gN (UL73) were amplified by nested PCR (nPCR). The amplicons were digested by restriction enzymes including MboⅠ, ScaⅠ and SalⅠ. Then, the restricted fragment length polymorphisms were further analyzed on 4% agarose gel. The relationships between HCMV genotypes and the morbidity and mortality of acquired immune deficiency syndrome (AIDS) were investigated via a prospective study. Results Among the 359 patients with HIV infection, 28 subjects were positive for the HCMV pp65 antigenemia assay. The HCMV gN genotypes in 20 patients with active HCMV infection were distributed as: gN-3a (4/20, 20%), gN-1 (4/20, 20%), gN-4d (1/20, 5%), gN-4b (1/20, 5%) and mixed infection (10/20, 50%). Patients with HCMV-HIV co-infection were more likely to develop AIDS during the follow-up period (RR=9.78). Patients harboring HCMV gN-1 and gN-4 genotypes would seem likely to have 4.6 times of chance leading to AIDS-associated death than those harboring other HCMV gN genotypes. Conclusion HCMV infection (especially gN-1 and gN-4 genotypes) might accelerate the progression of HIV infection. Key words: HIV; HCMV; Restricted fragment length polymorphism analysis (RFLP)