A 29-year-old woman with aplastic anemia who complained of visual disturbances and pain in the right eyeball was diagnosed as having cytomegalovirus (CMV) retinitis based upon the characteristic retinal changes and isolation of CMV. She received treatment with ganciclovir (GCV), and the retinitis initially responded for several months. However, the patient was found to have CMV lesions in the left eye followed by neurological symptoms. The CMV isolated just before her death was approximately 20 times more resistant to GCV than that isolated previously, suggesting that the GCV-resistant CMV had developed during the long-term treatment with GCV.