PURPOSE. Late-onset central areolar choroidal dystrophy (CACD) may easily be confused with geographic atrophy (GA) in AMD. To detect discerning features, the morphologic changes in CACD patients and in AMD patients were assessed with confocal scanning laser ophthalmoscopy (cSLO), fundus autofluorescence (FAF), and spectral-domain optical coherence tomography (SD-OCT). METHODS. A total of 30 CACD patients with identified PRPH2 gene mutations were analyzed and compared to 19 patients with early AMD and 13 patients with AMD-associated GA. The presence of drusen and pigment clumping was determined with color fundus photography. High-resolution in vivo imaging was performed with cSLO and SD-OCT. FAF images and SD-OCT volume scans were analyzed in each study eye. RESULTS. On FAF, a speckled FAF pattern occurred significantly more often in CACD (85%) than in early AMD (5.6%; P < 0.0001). There was a significantly higher frequency of sub-RPE deposits in eyes with AMD than in eyes with CACD (36.8% versus 2.1% of scans, P = 0.0019). Reticular drusen could be visualized by SD-OCT and FAF imaging in 52.6% of the eyes with early AMD and in 100% of the eyes with GA, whereas this drusen phenotype did not manifest in eyes with CACD. CONCLUSIONS. Although outer retinal atrophy is the clinically common feature in advanced CACD as well as GA, there are microstructural alterations on high-resolution SD-OCT and FAF imaging that allow for the differentiation between CACD and AMD. The findings may help to identify patients in whom a diagnostic PRPH2 screening is warranted. (ClinicalTrials. gov number, NCT00393692.) (Invest Ophthalmol Vis Sci. 2011;52:8908-8918) DOI:10.1167/iovs.11-7926