Canine chondrodysplasia is a heritable defect of endochondral ossification characterized by disproportionately short limbs. It is directly linked to significant health concerns, such as intervertebral disc disease. Some human skeletal dysplasias exhibit similar disproportionate dwarfisms and are associated with mutations in the RMRP and SHOX genes. These phenotypic similarities indicated RMRP and SHOX as candidate genes in dogs. They were sequenced in three chondrodysplastic and three normal-legged breeds. Single nucleotide polymorphisms in the promoter regions of both genes and in exon 2 of SHOX were found in affected and unaffected breeds, indicating that they are not associated with canine chondrodysplasia.