The Kelpie is an Australian derived dog breed developed for herding. Cerebellar abiotrophy (CA) is a movement disorder which results in early onset ataxia, and was first documented in Australian Kelpie (AK) and Australian Working Kelpie (AWK) dog breeds in 1989. The cerebellum controls movement and coordination and is affected in CA by a loss or failure of development of cerebellar Purkinje and granular cells, but with a degree of variation in severity. A genome-wide analysis study has mapped CA in working Kelpies to six associated regions across 5 chromosomes: 3, 22, 34, 35 and X, containing eight putative candidate genes. These results suggest that CA in the AWK is a Mendelian disorder with a complex genetic basis. Analysis of genome sequences from one CA affected and five unaffected Kelpies identified 12 protein-coding, and 12 regulatory single nucleotide polymorphisms (SNP) within these candidate genes. Confirmation of these variants and determination of allele frequencies in a larger number of cases and healthy control dogs is underway. Further work will involve sequencing more CA affected working Kelpies employing the 100 base paired-end Illumina HiSeq 2000 sequencing, to identify additional SNP and potential insertion-deletion events.