Blood flow in microvessels differs significantly from that of red blood cells (RBC) flowing through long, straight glass tubes in vitro. The in vivo situation is characterized by the presence of plasma favoring aggregation, by the irregular geometry of vessel segments, and by frequent branching points. Here, a method is presented to characterize flow patterns in microvascular blood flow during intravital microscopy based on Fourier analysis of recorded light intensity patterns. The interpretation of the resulting power spectra in terms of pattern size distribution was validated by model experiments employing artificial textures and by reverse transformation of idealized spectra. The determined size of RBC flow patterns in microvessels ranged from ∼8 μm in capillaries to ∼14 μm in vessels of >30 μm. With increasing shear rate above ∼100 s−1 pattern size increased, possibly reflecting formation of short-lived flow clusters. Below ∼100 s−1 an increase of pattern size with decreasing shear rate was found in experiments using local occlusion and treatment with high-molecular-weight dextran, suggesting the formation of aggregates. The dynamic process of generation and destruction of RBC flow patterns could well contribute to flow resistance in vivo in peripheral vascular beds.