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Hormone analysis techniques using non\u2010invasive sample collection have been vigorously developed for endangered species, from whom blood sampling is prohibited, or from species that are otherwise difficult to handle in a laboratory setting. Because there are interactions between glucocorticoids and thyroid hormones (T3 and T4), reducing the animal's \u201cdistress\u201d during sample collection is imperative. Measurement of fecal T3 provides less sensitive, baseline information regarding thyroid function while permitting a non\u2010invasive technique for more frequent sampling. We demonstrated that using a methanol extraction protocol produced the most reliable fecal T3 measurement in an enzyme\u2010linked immunosorbent assay (ELISA). We found that during a thyroid hormone\u2010treated state, fecal and plasma T3 measurements from mice are directly related, while during a methimazole\u2010treated state, fecal and plasma T3 measurements from mice are inversely related. 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