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Hormonally mediated effects on the female reproductive system may manifest as pathologic changes of endocrine-responsive organs and altered reproductive function. Identification of these effects requires proper assessment, which may include investigative studies to profile female reproductive hormones. Here, we briefly describe normal hormonal patterns across the estrous or menstrual cycle and provide general guidance on measuring female reproductive hormones and characterizing hormonal disturbances in nonclinical toxicity studies. Although species used in standard toxicity studies share basic features of reproductive endocrinology, there are important species differences that affect both study design and interpretation of results. Diagnosing female reproductive hormone disturbances can be complicated by many factors, including estrous/menstrual cyclicity, diurnal variation, and age- and stress-related factors. Thus, female reproductive hormonal measurements should not generally be included in first-tier toxicity studies of standard design with groups of unsynchronized intact female animals. Rather, appropriately designed and statistically powered investigative studies are recommended in order to properly identify ovarian and/or pituitary hormone changes and bridge these effects to mechanistic evaluations and safety assessments. This article is intended to provide general considerations and approaches for these types of targeted studies.