Purpose To measure choroidal thickness on spectral-domain optical coherence tomography (SD OCT) images using automated algorithms and to correlate choroidal pathology with retinal changes attributable to diabetic macular edema (DME). Design Post hoc analysis of multicenter clinical trial baseline data. Methods SD OCT raster scans/fluorescein angiograms were obtained from 284 treatment-naïve eyes of 142 patients with clinically significant DME and from 20 controls. Three-dimensional (3D) SD OCT images were evaluated by a certified independent reading center analyzing retinal changes associated with diabetic retinopathy. Choroidal thicknesses were analyzed using a fully automated algorithm. Angiograms were assessed manually. Multiple endpoint correction according to Bonferroni-Holm was applied. Main outcome measures were average retinal/choroidal thickness on fovea-centered or peak of edema (thickest point of edema)–centered Early Treatment Diabetic Retinopathy Study grid, maximum area of leakage, and the correlation between retinal and choroidal thicknesses. Results Total choroidal thickness is significantly reduced in DME (175 ± 23 μm; P = .0016) and nonedematous fellow eyes (177 ± 20 μm; P = .009) of patients compared with healthy control eyes (190 ± 23 μm). Retinal/choroidal thickness values showed no significant correlation (1-mm: P = .27, r2 = 0.01; 3-mm: P = .96, r2 < 0.0001; 6-mm: P = .42, r2 = 0.006). No significant difference was found in the 1- or 3-mm circle of a retinal peak of edema–centered grid. All other measurements of choroidal/retinal thickness (DME vs healthy, DME vs peak of edema–centered, DME vs fellow, healthy vs fellow, peak of edema–centered vs healthy, peak of edema–centered vs fellow eyes) were compared but no statistically significant correlation was found. By tendency a thinner choroid correlates with larger retinal leakage areas. Conclusions Automated algorithms can be used to reliably assess choroidal thickness in eyes with DME. Choroidal thickness was generally reduced in patients with diabetes if DME is present in 1 eye; however, no correlation was found between choroidal/retinal pathologies, suggesting different pathogenetic pathways.