Background/Objectives The purpose of this study was to evaluate macular ganglion cell layer-inner plexiform layer (GCL-IPL) and choroidal thickness in early age-related macular degeneration (AMD) in eyes with subretinal drusenoid deposits (SDD). Subjects/Methods Comprehensive ophthalmological examination was performed. Near infrared reflectance and raster images using enhanced depth imaging were acquired with spectral domain optical coherence tomography. Drusen and SDD were diagnosed based on raster scans and near infrared reflectance. GCL-IPL maps were generated with automated segmentation and choroidal thickness maps were obtained by manually delineating the choroid-scleral boundary. Results Forty-eight eyes from 48 patients (mean age 77.5 ± 5.7, range 68-90 years) with a diagnosis of early AMD and 42 eyes of 42 age-matched control subjects (mean age 76.9 ± 5.7, range 67-88 years) were included. Of these, 28 eyes (58.3%) had drusen alone, 4 eyes (8.3%) had SDD alone, and 16 eyes (33.3%) had drusen associated with SDD. Compared with controls, average choroidal thickness was significantly decreased in AMD eyes (P < 0.05). There was no significant difference in choroidal thickness in eyes with SDD with respect to those with drusen alone. GCL-IPL thickness was reduced in an annular pattern at the 3 and 6 mm macular areas in AMD patients with respect to controls (P < 0.05). GCL-IPL thickness at 3 mm was significantly reduced in eyes with SDD with respect to those with drusen alone (P = 0.03). Conclusions The GCL-IPL is reduced in thickness with an annular pattern in early AMD and is significantly thinner in eyes with SDD.