Blood flow and blood-endothelium interactions correspond with the genesis of cardiovascular diseases. Therefore, quantitative analysis of blood flow dynamics at the microcirculation level is of special interest. Regulatory mechanisms mediated by blow flow have been studied in detail using in vitro approaches. However, these mechanisms have not been fully validated in vivo due to technical limitations that arise when quantifying microhemodynamics with the required level of detail. Intravital microscopy combined with high-speed video recordings has been used for the analysis of blood flow in small blood vessels of chronic and acute experimental tissue preparations. This tool can be used to study the interaction between the flowing blood and the vessel walls of arterioles and venules with sufficient temporal and spatial resolution. Our objective was to develop a simple and robust cross-correlation algorithm for the automatic analysis of high-speed video recordings of microcirculatory blood flow. The algorithm was validated using in vitro and in vivo systems. Results indicate that the algorithm's ability to estimate the velocity of local red blood cells as a function of blood vessel radius is highly accurate. They thereby suggest that the algorithm could be used to explore dynamic changes in blood flow under different experimental conditions including a wide range of flow rates and hematocrit levels. The algorithm can also be used to measure volumetric flow rates, radial velocity profiles, wall shear rate, and wall shear stress. Several applications are presently explored, including the analysis of velocity profiles in the branches of arterial bifurcations. This work demonstrates the robustness of the cross-correlation technique in various flow conditions and elucidates its potential application for in vivo determination of blood flow dynamics in the microcirculation.