The genetic basis of body weight in the mouse was investigated by measuring frequency changes of microsatellite marker alleles in lines divergently selected for body weight from a base population of a cross between two inbred strains. In several regions of the genome, sharp peaks of frequency change at linked markers were detected, which suggested the presence of single genes of moderate effect, although in several other regions, significant frequency changes occurred over large portions of chromosomes. A method based on maximum likelihood was used to infer effects and map positions of quantitative trait loci (QTLs) based on genotype frequencies at one or more marker loci. Eleven QTLs with effects in the range 0.17-0.28 phenotypic standard deviations were detected; but under an additive model, these did not fully account for the observed selection response. Tests for the presence of more than one QTL in regions where there were large changes of marker allele frequency were mostly inconclusive.