Purpose: To detect the cytomegalovirus (CMV) genome by PCR in the aqueous humor, blood leukocytes and vitreous of patients affected by retinitis and immune recovery uveitis (IRU). Methods: A PCR for CMV genome detection was carried out with the aqueous humor, vitreous and blood leukocytes of 54 patients with retinitis, including 25 HIV-infected patients presenting CMV retinitis in different stages (active lesion 6 cases, healed lesion 14 cases and IRU 5 cases), and 29 non-HIV-infected patients (retinitis unrelated to CMV) as negative controls. Results: The CMV genome was detected in the vitreous, aqueous humor and blood leukocytes of 3 out of 6 HIV-infected patients, presenting active lesions in the retina. No CMV genome was detected in the vitreous, aqueous humor and blood leukocytes of the 5 HIV-infected patients presenting IRU. Conclusions: CMV genome detection by PCR in aqueous humor could be used as a specific and highly predictive technique for confirmation of this infection in the retina. The absence of CMV, based on the results of PCR done in clinical samples of the 5 IRU cases, does not confirm the hypothesis of a viral replication in the vitreous body and aqueous humor of these patients.