Accurate diagnosis of both age-related macular degeneration (AMD) and inherited retinal diseases (IRD) with macular atrophy is important because treatments for both conditions are emerging. Phenotypical similarities between macular atrophy associated with AMD (geographic atrophy, GA) and IRD-associated atrophy exist, which can make accurate diagnosis challenging in clinical practice. Misdiagnosis may lead to inappropriate treatment strategies and missed opportunities for disease-specific interventions. A retrospective clinical review of medical records of people diagnosed with AMD between 1995 and 2023 from a large multidisciplinary private ophthalmic practice in Australia was undertaken to identify cases of patients diagnosed with geographic atrophy without drusen, which was then further assessed for potentially missed IRD with macular atrophy. Flagged cases were presented to experts in AMD and IRD to establish a most-likely diagnosis. Cases without consensus between graders were grouped into most-likely diagnosis by a third senior retinal clinician. Of the 1136 cases reviewed, the possible rate of misdiagnosis observed was 1.9%, with 1.0% representing potentially missed IRDs, most commonly pattern dystrophy (0.5%). A multi-modal approach, including clinical features and patient history, is important to limit the possibility of misdiagnosis of GA, and identify a subset of patients who might benefit from genetic testing prior to considering possible treatments.