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To evaluate corneal morphology using ultrasonic pachymetry (USP), Fourier-domain optical coherence tomography (FD-OCT), and in vivo confocal microscopy (IVCM) in 2 related canine breeds—German shorthaired pointers (GSHPs) and German wirehaired pointers (GWHPs)—with and without corneal endothelial dystrophy (CED). This condition is characterized by premature endothelial cell degeneration leading to concomitant corneal edema and is similar to Fuchs endothelial corneal dystrophy.Corneas of 10 CED-affected (4 GSHP and 6 GWHP) and 19 unaffected, age-matched (15 GSHP and 4 GWHP) dogs were examined using USP, FD-OCT, and IVCM. A 2-sample t test or Mann–Whitney rank-sum test was used to statistically compare parameters between both groups. Data are presented as mean ± SD or median (range).Central corneal thickness determined using USP was significantly greater in CED-affected than in unaffected dogs at 1179 (953–1959) and 646 (497–737) μm, respectively (P < 0.001). Central epithelial thickness was found to be significantly decreased in CED-affected versus unaffected dogs at 47 ± 7.1 and 55 ± 7.1 μm, respectively (P = 0.011), using FD-OCT. With IVCM, corneal endothelial density was significantly less (P < 0.001) in 5 dogs with CED versus 19 unaffected controls at 499 ± 315 versus 1805 ± 298 cells/mm2, respectively. CED-affected dogs exhibited endothelial pleomorphism and polymegethism, whereas CED-unaffected dogs had regular hexagonal arrangement of cells.GSHPs and GWHPs with CED exhibit marked differences in corneal morphology when compared with age-matched control dogs. These 2 CED-affected breeds represent spontaneous, large animal models for human Fuchs endothelial corneal dystrophy.