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Digital particle image velocimetry (DPIV) is an extremely powerful technique for quantitative flow measurements. In order to perform hemodynamic measurements in embryonic hearts, DPIV analysis was performed on both Zebrafish (Danio rerio) and Quail (Coturnix coturnix japonica) embryos. A protocol for performing DPIV at the microscale with microscopy and high-speed imaging is presented. Results show the presence of vortices and jets at low Reynolds numbers implying a high shear on vessel walls, and suggest that hemodynamics may play an important role in future heart development studies.