In this study, we described a large, densely mapped, segregating F2 mouse population designed to study the genetic regulation of several traits associated with the so-called metabolic syndrome. Several groups, including ours, have reported the advantage of combining traditional genetics with genome-wide gene expression analysis for the dissection of complex traits. This study improved on past models by including over 300 animals (three times the size of previous studies) of both sexes, allowing for the incorporation of sex-specific effects on underlying genetic regulation.