IMPUTE is a program for estimating (”imputing”) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. There are currently three different versions of the IMPUTE software available for download: version 0.5 implements the methodology described in Marchini et al. (2007); version 1 is essentially the same as version 0.5, with a couple of added features; and version 2 implements a major extension that was introduced in Howie et al. (2009).