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Fluctuating asymmetry (FA), typically measured by variation in the differences between right and left sides of bilateral traits, is commonly used to assess developmental instability (DI) in populations. A previous quantitative trait locus (QTL) investigation using an F2 intercross mouse population found little evidence of individual loci affecting FA in mandible size, but an abundance of epistatic interactions between loci. Here we extend this work by testing whether these patterns replicate in an F3 population derived from the same intercross. Using a large number of molecular markers genotyped in over 1200 mice, we uncovered significant interactions between loci (QTLs) affecting FA in mandible size (and shape). Epistasis contributed roughly 20% of the variation in FASIZE and 19% of the variation in FASHAPE at the 0.0001 probability level alone, and was comparable to that previously estimated for the F2 mice, and much greater than that generated from the few single-locus QTLs affecting the mandible FA traits. The positions of the single-locus and epistatic QTLs for FA that we discovered suggested that logical candidate genes for DI are those controlling size or shape in the traits themselves, and that they may be interacting with genes for heat shock proteins.