We estimated the incidence of the first episodes of cytomegalovirus (CMV) disease in the Aquitaine cohort of HIV-infected subjects, south-western France. Cases were retrospectively investigated using standardized definition criteria. Retinitis was confirmed by an ophthalmologist. Gastro-intestinal lesions were confirmed histologically. Encephalitis was histologically confirmed; it was considered possible if TDM or magnetic resonance imaging (MRI) and symptomatology suggested this diagnosis. Pneumopathy was probable in case of hypoxemia, interstitial X-Ray images and response to CMV treatment; it was confirmed if intranuclear inclusions were identified on biopsy or brushing specimen. In the cohort (n = 3525) followed for an average of 46 months, 158 patients had a first episode of CMV disease. The cumulative incidence was 4.5% and the incidence rate (IR) 1.2 per 100 person-years. The IR was higher for homosexuals (2.0) than for heterosexuals (1.0) and intravenous drug users (0.5). Retinitis was the most frequent site (90 cases), followed by digestive system (40), lung (three confirmed and 17 probable) and central nervous system (eight confirmed and three possible). Sixty-eight percent of the patients were at the AIDS stage when CMV disease was diagnosed, with a mean CD4 count of 42/mm3. The cumulative probability of developing CMV disease 2 years after falling below 200 CD4 lymphocytes/mm3 was 8.0%. Retinitis is by far the most common site for CMV disease. Homosexual transmission of HIV, clinical AIDS and low CD4 count are associated with the occurrence of the first episode of CMV disease.