The recent release of the first phase of the Haplotype Mapping project (Nature, Oct. 26, 2005 - see also, e.g. NY Times, Oct. 27), and the rapid reduction in genotyping costs, open new directions and opportunities in the study of complex genetic disease such as cancer or Alzheimer’s disease. The advances in genotyping technology set new computational and statistical challenges due to the increased size of the datasets analyzed. In this talk I will discuss some of the computational challenges that are set by these studies, and the current and potential impact of computation on the understanding of complex diseases. In particular, I will describe recent results on genotype phasing, population stratification issues (clustering), and algorithmic issues involved in the study design.