The genetic contribution to a number of neurological disorders is thought to be complex in nature, disease risk being driven by a combination of risk alleles commonly present in the human genome. Recently the completion of stages I and II of the international Haplotype Map project and the availability of high-plex SNP assays has made genome wide assay of common genetic variability a realistic endeavor. We are applying genome wide association analysis using 500,000SNPs to a Parkinsons disease cohort from the NINDS funded neurogenetics repository. We have developed and implemented the necessary hardware and software infrastructure to store and manipulate the 2 billion datapoints associated with these experiments. The data the experiments analysing Parkinsons disease are complete and have recently been published; we are now nearing completion of the second stage of this work, analysing 1000 Parkinsons disease cases and 1000 neurologically normal controls, these data will be posted at dbGAP for mining an augmentation by interested researchers.