The circadian glucocorticoid rhythm provides important information on the functioning of the hypothalamic-pituitary-adrenal axis in individuals. Frequent repeated blood sampling can limit the kinds of studies conducted on this rhythm, particularly in small laboratory rodents that have limited blood volumes and are easily stressed by handling. We developed an extraction and assay protocol to measure fecal corticosterone metabolites in repeated samples collected from undisturbed male and female adult Sprague-Dawley rats. This fecal measure provides a non-invasive method to assess changes in corticosterone within a single animal over time, with sufficient temporal acuity to quantify several characteristics of the circadian rhythm: e.g. the nadir, acrophase, and asymmetry (saw-tooth) of the rhythm. Males excreted more immunoreactive fecal corticoids than did females. Across the estrous cycle, females produced more fecal corticoids on proestrus (the day of the preovulatory luteinizing hormone surge) than during estrus or metestrus. These results establish a baseline from which to study environmental, psychological, and physiological disturbances of the circadian corticosterone rhythm within individual rats.