Despite a consistent body of research on the neuroactive effects of reproductive hormones, and the growing attention given to menstrual cycle studies, it is difficult to draw general conclusions about the menstrual cycle’s impact on brain and behavior. This is partially due to the lack of systematic methodology and consistent experimental design across studies, alongside large inter- and intra-individual variability in hormonal patterns. In this Methods Hour, we will delve into the challenges of researching the human menstrual cycle and take a closer look at hormonal suppression (i.e., oral contraceptives) research. Is the menstrual cycle different from other contextual factors (internal and external) that shape the human brain? Is there a correct way of measuring it? How do the biomedical and social sciences benefit from the study of reproductive hormones?