Even though the trade-off between the benefits and risks of blood transfusion has been discussed for the last several decades, it requires further understanding of the rheological changes in stored blood that include the alteration of red blood cell (RBC) aggregation. The RBC aggregation of stored blood in its autologous plasma was monitored through the storage period (35 days). The critical shear stress, as a measure of RBC aggregation, was determined by using a microfluidic aggregometer. Blood was processed into a blood bag containing the anticoagulant CPDA1 and stored at $4^{circ}C$. It was subjected to assays after zero, seven, 14, and 35 days. The critical shear stress for stored blood did not change up to 14 days of storage but exhibited a significant decrease after 35 days of storage. These results were identical to those of the conventional aggregation index (AI). Also, in the alteration of RBC aggregation for blood storage, the effect of the plasma factor was slightly stronger than that of the cellular factor. Through the present study, the critical shear stress as a new measure of RBC aggregation may help to monitor and control the quality of blood storage.