Significance Chondrodystrophy, characterized by short limbs and intervertebral disc disease (IVDD), is a common phenotype in many of the most popular dog breeds, including the dachshund, beagle, and French bulldog. Here, we report the identification of a FGF4 retrogene insertion on chromosome 12, the second FGF4 retrogene reported in the dog, as responsible for chondrodystrophy and IVDD. Identification of the causative mutation for IVDD will impact an incredibly large proportion of the dog population and provides a model for IVDD in humans, as FGF-associated mutations are responsible for IVDD and short stature in human achondroplasia. This is a report of a second retrogene copy of the same parental gene, each causing complementary disease phenotypes in a mammalian species.