To describe the clinical and genetic characteristics of pachychoroid geographic atrophy (GA) and to compare them with those of conventional GA associated with age-related macular degeneration (AMD). Observational case series. Ninety-two eyes of 92 consecutive patients with GA who underwent a full ophthalmologic examination, including best-corrected visual acuity measurement, spectral-domain OCT, and fundus autofluorescence imaging. Their blood samples were genotyped for the major AMD-associated single nucleotide polymorphisms. Pachychoroid GA was diagnosed if all of the following criteria were met: (1) GA in either eye; (2) clinical and anatomic features of the pachychoroid phenotype, such as reduced fundus tessellation and dilated choroidal vessels; and (3) no drusen in both eyes. Drusen-related GA was defined as conventional GA. Comparison of clinical and genetic characteristics between pachychoroid GA and conventional GA. Twenty-one patients (22.8%) were diagnosed with pachychoroid GA. These patients were significantly younger than those with conventional GA (mean age, 70.5 vs. 78.5 years; P < 0.001), had a smaller GA area (mean, 0.9 mm2 vs. 4.0 mm2; P < 0.001, age-adjusted), had greater subfoveal choroidal thickness (mean, 353.3 μm vs. 175.6 μm; P= 0.009, age-adjusted), and were more likely to have choroidal vascular hyperpermeability (47.4% vs. 6.3%; P < 0.001). Pseudodrusen were found in 40 of 71 patients (56.3%) with conventional GA, but not in any of the patients with pachychoroid GA. The risk allele in ARMS2 A69S was less common in patients with pachychoroid GA than in those with conventional GA (31.6% vs. 68.8%; P < 0.001). The genetic risk score calculated from the single nucleotide polymorphisms of 11 AMD susceptibility genes indicated that patients with pachychoroid GA were less genetically prone to AMD than the conventional GA group (P= 0.001). Pachychoroid GA was diagnosed in 23% of patients with GA. Differences in the phenotypic and genetic characteristics of pachychoroid GA and conventional GA were identified. These 2 conditions should be differentiated when considering prevention and therapeutic strategies.