Although there typically is little additive genetic variation for fluctuating asymmetry (FA), or variation in nondirectional differences between left and right sides of bilateral characters, several investigators have hypothesized that FA may have an epistatic genetic basis. We tested this hypothesis by conducting a whole genome scan of FA of size and shape of the mandibular molars in house mice from an F2 intercross population generated from crossing the Large (LG/J) and Small (SM/J) inbred strains. Although no individual genes (QTLs=quantitative trait loci) on any of the 19 autosomes significantly affected FA for centroid size, and only two affected shape FA, a number of pairwise combinations of QTLs exhibited significant epistasis for FA in both molar size and shape. The QTLs involved in these interactions differed for FA in molar size versus FA in molar shape, but their epistatic contributions to the total variance was nearly the same (about 20%) for FA in both molar characters. It was noted that the genetic architecture of FA in the molar characters, consisting of little or no additive genetic variance but an abundance of epistatic genetic variance, is consistent with that of other typical fitness components such as litter size.