Individual identification is a common method used in animal research. This study was designed to examine if commonly used identification systems (i.e., leg bands, wing bands, neck tags, and livestock markers) have different effects on hens' behavioral and physiological homeostasis. At 18 wk of age, hens were paired in all combinations of treatments and control (unmarked hens; n = 10) in a novel cage for 5 trials of 1 h each to test the effects of identification markers on social behaviors. Wing-banded hens tended to exhibit increased feather pecking compared with control hens (P < 0.10), suggesting a slight increase in social stress. No effect of identification treatment was evident on frequency of aggressive behaviors (P > 0.10). At 20 wk of age, absolute fluctuating asymmetry (FA), but not relative FA, of shank length and width was more significant in leg-banded hens (P < 0.05) and tended to be significant in wing-banded hens (P < 0.10), compared with control hens. Asymmetry of the shank is often a result of high stress levels, including social stress. Body weight measured at 20 wk of age showed that hens with leg bands were significantly lighter than control hens (P < 0.05), possibly as a result of decreased access to resources, increased metabolism, or decreased appetite due to elevated stress. Increased absolute FA and decreased BW could be evidence of a disruption of the hens' physiological homeostasis due to increased stress. Hens with leg bands also tended to have lower percentage of heterophils (P < 0.10), indicative of increased stress and reduced immunocompetence. Our findings provide clear evidence of the negative effects of wing and leg band identification systems on hens' well-being, altering both physiological and behavioral homeostasis. Without knowledge of the effects, the use of individual identification systems could lead to misinterpretation of experimental results.