To examine the epidemiology, treatment patterns, and costs of cytomegalovirus (CMV) retinitis treatment in the post-HAART (highly active antiretroviral therapy) era, a retrospective cohort study was performed using data from US managed-care plans from 1997-2002. Cases with CMV retinitis were defined by requiring diagnosis codes for HIV (or AIDS), CMV, and retinitis and claims for anti-CMV treatment. Costs of oral, intravenous, and intraocular treatment periods were examined. The incidence of enrolled HIV or AIDS cases increased from 7 per million members in 1997 to 150 per million members in 2001. The incidence of CMV retinitis decreased from 23 per 10,000 HIV or AIDS cases in 1997 to 8 per 10,000 HIV or AIDS cases in 2001. The average duration of a CMV episode was 192 days and the average cost was 19,576 US dollars. In a multiple linear regression model adjusting for age, gender, insurance type, geographic region, HAART use, and co-existing AIDS-defining illnesses, intraocular and oral treatment periods saved 7135 and US dollars and 6866 US dollars, respectively, per treatment period compared with intravenous treatment (P < 0.05). The incidence of CMV retinitis decreased in this managed-care population during the post-HAART era. Use of oral or intraocular treatment saves costs compared with intravenous treatment in a managed-care environment.