There is substantial evidence that the ovarian sex hormones, estrogen and progesterone, which vary considerably over the course of the human female lifetime, contribute to changes in brain structure and function. This structured, quantitative literature reviews aims to summarize neuroimaging literature addressing physiological variation in brain macro- and microstructure across an array of hormonal transitions including the menstrual cycle, use of hormonal contraceptives, pregnancy, and menopause. Twenty-five studies reporting structural neuroimaging of women, addressing variation across hormonal states, were identified from a structured search of PUBMED and were systematically reviewed. Although the studies are heterogenous with regard to methodology, overall the results point to overlapping areas of hormone related effects on brain structure particularly affecting the structures of the limbic system. These findings are in keeping with functional data that point to a role for estrogen and progesterone in mediating emotional processing.