Identification of genes underlying complex traits presents a challenge to which geneticists have responded with many diverse approaches. A common feature of these approaches is that different research groups must, on a case-by-case basis, replicate similar efforts in recruitment, genetic characterization, and analyses. To avoid this expensive “churning,” an alternative approach has been proposed: production of an experimental genetic reference population, the Collaborative Cross, in which both genetic diversity and mapping power are maximized. Since this population consists of inbred mouse strains, further advantages are that it is essentially infinitely reproducible; genetic characterization needs to be performed only once; and the founder strains' genomes have been or will be sequenced, allowing imputation of allele sequences of all members of the reference population. Here we describe the establishment of such a genetic reference population, which we dub “The Gene Mine.” Over 1000 genetically distinct lines have been established, descended from eight diverse founder strains. Preliminary phenotypic ascertainment of these strains indicates unexpected variability arising from independent assortment of genetic variants. The Gene Mine will be a powerful resource for characterization of essentially any mouse phenotype that has a genetic basis.