The present invention identifies the changes in gene expression associated with Parkinson's Disease by examining multiregional gene expression from normal brain and brain of Parkinson's Disease. The present also identifies the changes in gene expression associated with Parkinson's Disease by examining the expression of genes from normal blood and from the blood of patients with Parkinson's Disease. In another aspect, the present invention identifies expression profiles which serve as useful diagnostic markers as well as markers that can be used to monitor disease states, disease progression, drug toxicity, drug efficacy and drug metabolism.