Blinding inherited eye diseases affect millions of people worldwide. Despite a large number of gene discoveries, many patients lack the molecular description of their condition. The domestic dog has become a widely used model to study inherited eye disease genetics and therapeutics during the past 15 years, and nearly 50 genes have been implicated across breeds. Despite a continuous discovery of new causative variants across canine eye disease groups, the genetic cause in most cases is expected to remain unknown. We tested this hypothesis by screening 49 known variants in 194 dogs from 71 breeds affected with progressive retinal atrophy (PRA), glaucoma, or lens luxation and validated the results in additional 1180 dogs. We found that eleven variants in ten genes explained 28% of the studied cases. We also observed new PRA-affected breeds for the RPGRIP1 c.340_341insA29GGAAGCAACAGGATG variant, and clinical support for the pathogenicity of the PDE6A c.1940delA and ADAMTS10 c.2231G>A variants for PRA and glaucoma in two new breeds, respectively. Our findings indicate extensive genetic heterogeneity and the lack of molecular descriptions in more than two-thirds of the LL, glaucoma, and PRA cases by the current gene tests. There is an urgent need for discoveries that would be critical not only for veterinary molecular diagnostics and breeding programs but also for establishing models to characterize pathophysiology and new therapeutic options for the corresponding human eye disorders.