This work aims to develop a method for quantitatively analyzing red blood cell (RBC) aggregates under controlled flow conditions. Images of experiments are captured and processed in order to quantify aggregation. The experimental setup consists of RBC suspensions in blood plasma entrained by a phosphate-buffered saline solution in a 110 × 60 µm polydimethylsiloxane microchannel. The experiments are performed by varying the hematocrit (5, 10, and 15%) and the flow rate (Q = 5 and 10 µl/hr) in order to observe the effect of shear rate on RBC aggregation. Microchannel dimensions as well as fluid flow rates are determined using numerical simulations. The flow is visualized using a high- speed camera coupled to a micro particle image velocimetry system. Videos obtained with the high-speed camera are processed using a MATLAB program, with each frame analyzed separately. RBC aggregates are detected based on the image intensities and the connectivity between RBCs, using image processing techniques. The average aggregate size and distribution of RBCs for various aggregate sizes are determined for each of the shear rates and hematocrits. These aggregates are shown to be larger at low flow rates where the shear rate is small. Results from tests performed at high hematocrits also show larger RBC aggregates.