The most common and lethal birth defects affect the cardiovascular (CV) system. The mouse is a superior model for identifying and understanding mammalian CV birth defects, but there is a great need for tools that can detect early and subtle deficiencies in cardiac function in mouse embryos. We combined swept source optical coherence tomography (SS-OCT) with live mouse embryo culture protocols to generate structural two-dimensional and three-dimensional imaging and hemodynamic measurements in a live 8.5 day embryo just a few hours after the beginning of a heartbeat. Our data show that individual circulating blood cells can be visualized with structural SS-OCT, and using Doppler SS-OCT the velocity of single moving blood cells were measured during different phases of the heartbeat cycle. These results demonstrate that Doppler SS-OCT is an extremely useful tool for structural and hemodynamic analysis at the earliest stages of mammalian blood circulation.