Objectives: Premenopausal women have a significantly lower rate of atherosclerosis than men, an effect attributed to estrogen. The atheroprotective effects of estrogen are independent of circulating lipid levels and may be due to an effect on the vessel wall. Early on in atherosclerosis, circulating LDL is able to cross an intact endothelial monolayer by transcytosis and accumulate in the intima. Little is known about the mechanisms of transcytosis but using novel assays we recently discovered a role for the SR-BI and ALK1 receptors. We hypothesized that estrogen can attenuate LDL transcytosis by coronary artery endothelial cells. Approach and Results: Using a recently described assay based on total internal reflection fluorescence microscopy, we quantified transcytosis of LDL across human coronary artery endothelial cells treated with physiological concentrations of estrogen. Estrogen significantly attenuated LDL transcytosis by endothelial cells from male donors; the effect was ligand-specific as transcytosis of albumin was not affected. Estrogen caused down-regulation of endothelial SR-BI but not ALK1 and over-expression of SR-BI was sufficient to restore LDL transcytosis. Similarly, depletion of SR-BI by siRNA attenuated endothelial LDL transcytosis and prevented any further effect of estrogen. In contrast, treatment with estrogen had no effect on SR-BI expression by liver cells from a male donor. Inhibition of estrogen receptors α and β had no effect on estrogen-mediated attenuation of LDL transcytosis. However, estrogen’s effect was blocked by depletion of the G-protein coupled estrogen receptor (GPER) by siRNA. GPER was found to be enriched in endothelial cells compared to hepatocytes and is known to signal via transactivation of the epidermal growth factor receptor (EGFR); we observed that inhibition of EGFR also prevented the effect of estrogen on LDL transcytosis. Lastly, male mice demonstrated more vascular deposition of LDL than age-matched female mice after acute injection. Conclusions: Physiological concentrations of estrogen significantly inhibit LDL transcytosis by down-regulating endothelial SR-BI; this effect requires GPER. This may contribute to the lower rates of atherosclerosis in premenopausal women.