In the analysis of red blood cell (RBC) aggregation using optical detection, various shearing methods have been used to disperse RBCs in confined geometries. This study investigated RBC aggregation measurement in a microchip-stirring system by analysis of light transmission. A stirring-aided disaggregation mechanism in a microchip, consisting of a flat-cylindrical test chamber (D=4 mm, H=0.3 mm) and a magnetic stirrer (d=0.14 mm, l=2.2 mm), was used to generate a given shear which was large enough to disperse RBC aggregates, but not large enough to cause any mechanical hemolysis of cells. After stirring for 10 s followed by an abrupt halt of the stirring, the intensity of the light transmitted through a microchip was measured with respect to time and analyzed. A comparative study was conducted with varying test chamber height and hematocrit. The AI and t1/2 as typical aggregation indices obtained by analysis of transmitted light, which showed a good reproducibility (coefficient of variation (CV)<2.8%, n=10), also were found to be nearly independent of the chamber dimensions (CV<3.4%). The present aggregometry also showed the similar results of aggregation indices with varying hematocrits compared to those obtained using a laser-assisted optical rotational cell analyzer (LORCA). The essential feature of the present design is the adoption of a disposable microchip requiring a minimum blood sample volume as small as 6 mul, which enables it to be used easily in a clinical setting.