The successful discovery of genes that cause rare monogenic disorders has dominated our understanding of the genetic basis of neurodegenerative disease. The emergence of robust genome-wide association methodologies promises to explain the genetic etiology of the common sporadic forms of complex diseases. In addition to revealing the genetic susceptibility of neurodegenerative disease, genome-wide association studies (GWASs) should also be an unbiased generator of molecules that are relevant in disease pathogenesis. Despite this exciting potential, GWAS results have varied in their consistency and their ability to deliver these aims. The largest challenge that faces neuroscientists is the interpretation of the results of GWASs and the translation of the genetic findings into functional mechanisms that are biologically important in disease pathogenesis and, ultimately, treatment design. We examine recent results from GWASs of Alzheimer's disease and Parkinson's disease and explore their use and limitations. We further reflect on how these results may expedite progress in understanding and influencing the molecular pathogenesis of neurodegeneration.