One of the poorly understood clinical manifestations of cystic fibrosis (CF) is low body weight. Mice in which the CF causative gene, cystic fibrosis transmembrane conductance regulator (Cftr), has been knocked out reflect this as they are smaller than age-matched littermates. The variable weight of F2 Cftr -/- (CF) mice derived from a cross between congenic C57BL/6J and BALB/cJ Cftr heterozygotic mice permits the mapping of modifiers of this cystic fibrosis phenotype. In this report, quantitative trait loci (QTL) mapping was used to identify the chromosomal locations of genes that contribute to the body weight of 12-week-old F2 CF mice. Five loci of CF body weight were detected with four of the five acting in a sex-specific manner. Significant linkage of the phenotype to a region of Chromosome (Chr) 13 from D13Mit179 to D13Mit254 (LOD = 4.2) was established in female mice; and suggestive loci on Chrs 7 and 10 were identified. The weights of F2 male CF mice were suggestively linked to regions of Chrs 1 and 6, and to the same locus on Chr 7 as in female mice. The suggestive loci did not influence the weight of the limited set of control mice and thus are presumed to be CF specific in their effects. Further study of these putative CF body weight modifiers may provide insight on the pathogenesis of cystic fibrosis.