The mapping of complex trait loci in mice has recently become very popular thanks to dense genetic maps, better approaches to linkage analysis and the continued value of the mouse as a key model organism for human disease. Nevertheless, the ultimate goal remains very difficult to identify genes that underlie complex traits and to understand their function at a molecular level. In assessing the prospects of current efforts, it helps to review the findings of earlier studies of complex traits and, despite all the technology, to be reminded of the inherent benefits and limitations at the source of genetic variation: the laboratory mouse. With the right perspective it should be possible for geneticists analysing complex traits to take full advantage of the resources that the genome project will provide.