Post-menopausal hormone therapy increases the risk for venous thrombosis, and possibly myocardial infarction (MI) and ischemic stroke. However, most women using hormone therapy do not suffer thrombosis, and to date our ability to identify women at risk is limited. Thrombosis, arterial or venous, has 2 requisites: a vascular anomaly and a response of the hemostasis system to the anomaly. Consequently, experimental approaches to understand the pathophysiology of thrombosis require definition of vascular anatomy and function as well as characteristics of the blood within the context of genetic background, lifestyle choices and environmental exposures, which influence gene expression. Defining interactions among factors that affect individual propensity to thrombosis will allow physicians to better identify at-risk individuals, for example a woman contemplating estrogen therapy for symptoms of menopause, and prevent adverse thrombotic events.