Fluctuating asymmetry, which reflects small, random deviations from symmetry in otherwise bilaterally symmetrical characters, may be used as an indicator of developmental instability in humans and farm animals, and it may also be applicable as a stress indicator. We intended to find a method to allow the use of fluctuating asymmetry as a stress indicator in laboratory animals. That method had to be reproducible and reliable. Furthermore, its applicability in laboratory animals would be improved if it was possible to obtain measurements on the skin surface that correlated with results obtained by measuring the skeleton directly. Seven traits in mice and five traits in rats were evaluated for their applicability for measuring fluctuating asymmetry in mice and rats. Two out of the seven traits, i.e. the width of the joint between the third metatarsal bone and the digital bone on the hind paw, and the length of the incisor tooth at the top, were found to be reliable and reproducible for detecting fluctuating asymmetry in mice as well as in rats. Three out of the seven traits, i.e. the width of the carpal bones, the width of the joint between the tibia and the tarsal bones, and the length of the incisor tooth at the bottom, did express fluctuating asymmetry, but showed a poor day-to-day reproducibility. If the day-to-day reproducibility could be increased, these three traits might also be suitable for measuring fluctuating asymmetry in mice and rats. The last two traits, i.e. the length of ulna and the length of calcaneus plus metatarsal bone i.v., measured both on the skin surface and directly on the bone, did not express fluctuating asymmetry, and had a poor day-to-day reproducibility. These two traits are not suitable for measuring fluctuating asymmetry in mice and rats.