Confocal adaptive optics (AO) technology has enabled cellular level retinal imaging, including imaging of photoreceptors and blood flow. Adaptive optics scanning laser ophthalmoscopy (AOSLO) is a technology that provides high resolution and high contrast retinal images by correcting ocular aberrations. The authors present a case of polymerase chain reaction (PCR) positive cytomegalovirus (CMV) retinitis with AIDS that was monitored with AO technology and spectral domain OCT (SD-OCT). At initial presentation, the patient had fulminating retinitis characterised by a dense, white well demarcated geographical area of confluent opacification with retinal haemorrhages at the posterior pole. SD-OCT imaging showed that the inner segment ellipsoid line was disrupted within and on the border of the white and demarcated area. Even after HAART and valganciclovir, the atrophic area (defined as retinal thickness <100μm) progressed over a 32 month time period. An AO camera and AOSLO were used to evaluate the cone mosaic changes related to CMV retinitis. AO images showed a honeycomb like appearance 0.5mm above the fovea, which indicated direct visualisation of retinal pigment epithelium (RPE) cells and disappearance of the photoreceptor cells. At 32 months, AOSLO images showed the photoreceptors to be arranged in a disorderly fashion, and the normal cone mosaic arrangement could not be detected. In conclusion, this case has demonstrated that retinal atrophy caused by CMV retinitis can progress even after two years, and that cone photoreceptor cells are injured during the course of the disease, which can be monitored with AO and OCT imaging.