AIM: To investigate the etiology of ocular pathogens and to establish the various pathogens present in human immunodeficiency virus (HIV) patients with cytomegalovirus retinitis (CMVR). METHODS: A total of 17 HIV-infected patients with concomitant eye disorders were enrolled. Patients were divided into CMVR group (10 patients, 18 eyes) and non-CMVR group (7 patients, 9 eyes) based on clinical manifestations and the presence of cytomegalovirus (CMV)-DNA in ocular specimens. The viral load of CMV was assessed using polymerase chain reaction in aqueous humor, vitreous fluid, and peripheral blood samples of patients in the CMVR group. Additionally, peripheral blood CD4+ T cell counts were measured in both groups. RESULTS: In the CMVR group, the CMV-DNA load in the vitreous and aqueous humor samples was substantially higher than in the peripheral blood samples (P<0.01). CMV-DNA load in the aqueous humor and vitreous samples of the two eyes in the CMVR group was determined to be statistically significant (10 patients, 16 eyes, P=0.018, 0.012). Peripheral blood CD4+ T cell counts in the CMVR group were adversely linked with the CMV-DNA load in both the aqueous humor and peripheral blood (P=0.005, 0.048). Compared with the non-CMVR group, the peripheral blood CD4+ T cell count in the CMVR group decreased significantly (P=0.014). The peripheral blood CD4+ T cell count exceeded 300 cells/μL in 85.71% of non-CMVR patients, whereas it was below 100 cells/μL in 90.00% of the CMVR group. The intraocular specimens of the patients who underwent CMVR testing did not include any additional infections. CONCLUSION: In HIV-associated CMVR patients, there may exist alternative, yet unidentified, infection pathways for intraocular CMV in addition to the conventional route. The substantial difference in CMV-DNA load between the eyes of most CMVR patients suggests that CMV may originate from different sources in each eye. The proportion of peripheral blood CD4+ T cells in HIV patients is negatively correlated with the quantity of CMV viruses in their eyes. The peripheral blood count of <100 cells/µL indicates a considerable increase in the risk of concurrent CMVR. Multi-ocular pathogen presentations are uncommon in HIV individuals with CMVR.