Hot flashes represent the most common complaint among peri- and postmenopausal women. Over 60% of postmenopausal women experience hot flashes, and 10-20% of all postmenopausal women find them nearly intolerable. Despite the prevalence of hot flashes, their pathophysiology is not well understood. Treatment options include non-pharmacological approaches, hormonal interventions, and non-hormonal pharmacological agents. The most effective treatment for hot flashes is estrogen. The most promising non-hormonal treatments for hot flashes are selective serotonin or noradrenergic reuptake inhibitors (SSRI/SNRI). Although estrogen withdrawal is implicated in the initiation of hot flashes, and serotonin's role is well established in thermoregulation, the relationship between estrogen and serotonin is not known. Preclinical studies suggest that both estrogen and SSRI down regulate the serotonin transporter. Clinical studies that further delineate the relationship between effective treatments for hot flashes and the serotonin transporter may shed a new light into the pathophysiology of these symptoms and more importantly, into design of new-targeted treatments.