The distinctive and defining physical trait of the Scottish Fold cat breed is the characteristic ear phenotype. Scottish fold cats have ears which fold forward, this presumably reflecting lack of resilience of the pinna and auricular cartilages. There is convincing clinical, radiologic, histologic and genetic evidence that Scottish Fold cats have an underlying congenital defect which affects the structure and function of cartilage, resulting in progressive bone, joint and cartilage abnormalities that subsequently lead to progressive dysfunction. Cats develop a variable osteochondrodystrophy causing abnormal bone development likely through defective endochondral ossification, progressive osteoarthritis and lameness. From pedigree analyses and breeding experiments the phenotype has been shown to be inherited as autosomal monogenic dominant trait with variable expression. Thus, cats with two copies of the abnormal gene invariably have severe disease from an early age, whereas cats with one copy of the defective gene have disease which may vary from mild to moderate severity (in terms of extent of involvement and clinical progression). We applied a whole-genome SNP association mapping approach using a total of 78 cats (53 Scottish fold cats and 25 Scottish shorthairs). DNA samples were genotyped with the feline Illumina 63kSNP genotyping microarray. A genome-wide significant association on chromosome D3 has been identified and confirmed with fine structure mapping. The region contains a positional candidate gene involved in a wide range of inherited skeletal dysplasias in humans.