A new microchip-based aggregometer that uses a stirring-aided disaggregation mechanism in a microchip was developed to measure red blood cell (RBC) aggregation in blood and RBC suspensions. Conventional methods of RBC disaggregation, such as the rotational Couette system, were replaced with a newly designed stirring-induced disaggregation mechanism. Using a stirrer in a microchip, the aggregated RBCs stored in a microchip can be easily disaggregated. With an abrupt halt of the stirring, the backscattered light intensity can be measured in a microchip with respect to time. The time recording of the backscattered light intensity (syllectogram) shows an exponential decreasing curve representing the RBC aggregation. By analyzing the syllectogram, aggregation indices such as AI and M were determined. The results showed excellent agreement with LORCA. The essential feature of this design is the incorporation of a disposable microchip and the stirring-induced disaggregation mechanism.