The basal ganglia are a highly interconnected set of subcortical nuclei and major atrophy in one or more regions may have major effects on other regions of the brain. Therefore, the striatum which is preferentially degenerated and receives projections from the entire cortex also affects the regions to which it targets, especially the globus pallidus and substantia nigra pars reticulata. Additionally, the cerebral cortex is itself severely affected as are many other regions of the brain, especially in more advanced cases. The cell loss in the basal ganglia and the cerebral cortex is extensive. The most important new findings in Huntington's disease pathology is the highly variable nature of the degeneration in the brain. Most interestingly, this variable pattern of pathology appears to reflect the highly variable symptomatology of cases with Huntington's disease even among cases possessing the same number of CAG repeats.