The purpose of the present study was to examine the emergence of ganciclovir-resistant virus in the contralateral eyes of patients who received treatment for cytomegalovirus retinitis with either a ganciclovir implant plus oral placebo, a ganciclovir implant plus oral ganciclovir, or intravenous (iv) ganciclovir. Viral DNA was amplified from vitreous specimens and was assayed for UL97 and UL54 resistance mutations. Resistant viral genotypes were found in the contralateral eyes of 0 of 28 patients treated with a ganciclovir implant plus oral placebo, in 5 of 23 patients treated with a ganciclovir implant plus oral ganciclovir, and in 1 of 6 patients treated with iv ganciclovir. All resistance mutations were in codons 591, 592, or 594 of the UL97 gene. Treatment of unilateral cytomegalovirus retinitis with systemic ganciclovir decreases the risk of development of secondary sites of infection, but, in contralateral eyes that develop retinitis, this approach to treatment is associated with a higher prevalence of drug resistance, compared with treatment with the ganciclovir implant alone (P = .023; Fisher's exact test).