Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) is a recently recognised neurodegenerative disease with onset in late adulthood (1,2). Although many patients have been described with CANVAS (1,2), no genetic cause has been found for this apparently Mendelian disease. Gene discovery provides insights into the disease mechanism, possible therapeutic targets, and answers for the patients and their families. Here we present the largest genetic investigation of CANVAS patients to date, to our knowledge. All 20 patients are from New Zealand, either European or Maori, and included three sibling-pairs. Whether inheritance of CANVAS is dominant or recessive remains unclear. We performed whole exome sequencing on all patients, which was used for variant analysis, and other downstream applications. Principle component analysis of exome data revealed two distinct subpopulations in the cohort: one European and one Maori. To investigate this further, we performed identity-by-descent mapping, which showed cryptic relatedness within each subpopulation. Using this new information, we performed linkage analysis with inferred pedigrees based on the estimated relationship between patients. To assist in the search for the causative gene, we are using novel gene prioritisation methods based on FANTOM5 expression profiling.