With the availability of dense maps of anonymous and frequent SNPs spanning the whole human genome, genome-wide association studies are now becoming a reality. In this paper, we discuss the utility of these approaches to detect genetic risk variants involved in complex disease susceptibility and, in the best case scenario where a signal is detected, how helpful it will be to the understanding of the pathological process.European Journal of Human Genetics advance online publication, 13 December 2006; doi:10.1038/sj.ejhg.5201753.