Results/Conclusions To develop and validate this assay for Myotis sodalis, fecal samples were first collected from an abundant, non-endangered cogener, the little brown myotis (M. lucifugus), which served as a surrogate species. The procedure for extracting immunoreactive (ir) cortisol from fecal pellets of M. lucifugus was optimized for collection method, solvent type, duration of extraction, and recovery. Next, the fecal cortisol assay was validated for M. lucifugus by demonstrating an increase in fecal cortisol levels following an increase in plasma cortisol levels resulting from handling/blood-sampling stress. Finally, biochemical validations demonstrated that the assay accurately and precisely measured cortisol concentrations in fecal samples. Using these procedures, the presence of ir-cortisol was then demonstrated in feces from M. sodalis; values ranged from 0.35 to 3.89 ng/mg fecal mass. Continuing studies are being conducted to determine whether bats sampled at military sites have higher fecal ir-cortisol than bats sampled at non-impacted sites. The ability to assess stress is often an important aspect of ecological and conservation research. The procedure reported here will assist field researchers in efforts to quantify the physiological status of free-ranging and endangered bats and other mammals.