Hypodontia, congenital lack of one or a few teeth, is an autosomally inherited dominant trait. Homeobox genes MSX1 and MSX2 are expressed in presumptive dental tissues at the stage of initiation of tooth development. Recently, tooth development was shown to be inhibited in transgenic mice lacking a functional Msx1 gene. Here, we studied the relationship of the MSX1 and MSX2 genes to familial hypodontia in five Finnish families with a total of 20 affected individuals, by linkage analysis. The pairwise lod-scores regarding the intragenic microsatellites in the MSX1 and MSX2 genes at a recombination fraction of 0.0 were -3.1 and -3.0, respectively, thus excluding these genes as causative loci for hypodontia in these families.