Linkage disequilibrium (LD) has been used to map chromosomal regions regulating quantitative traits, also called quantitative trait loci (QTLs). With the increasing number of available mouse polymorphic genetic markers, LD can be estimated for the purpose of fine-mapping a given QTL or in the identification of novel QTLs. A whole-genome LD analysis was conducted for mapping mouse lung tumor susceptibility QTLs in 25 strains of mice with known susceptibility to lung cancer using 5638 genetic markers. A total of 63 markers were found to be significantly associated with lung tumor susceptibility, many of which were novel QTLs. This study demonstrates the feasibility of using LD to map QTLs on a whole genome level. Further characterization of the newly identified lung tumor susceptibility QTLs may lead to the identification of genes whose human homologue may predispose some individuals to lung cancer.