As the number of mammalian genomes to be completely sequenced continues to grow, researchers attempting to identify mutations responsible for inherited disease increasingly take advantage of studies undertaken in alternative species, usually humans, to identify and investigate previously identified "candidate genes" in their own species. This chapter describes the identification of microsatellites closely associated with candidate genes and their subsequent analysis in cohorts of samples segregating a disease or trait of interest for an association between the candidate genes and the condition under investigation.