Dental caries are initiated by the attachment of Streptococcus mutans aggregates to the surface of teeth. Bacterial adhesion to the interproximal space, the space between adjacent teeth, has not been investigated due to the lack of devices that mimic the space. Herein, we describe a method for determining the effect of shear stress and sucrose on the attachment of S. mutans aggregates to the interproximal space using microfluidic funnel device (μFFD). Using μFFD, the shear stress tolerance of sucrose-independent and sucrose-dependent S. mutans aggregates (larger than 50μm in diameter) trapped in the funnel was tested against various flow rates of saliva solution (5 to 50μl/min). Sucrose-independent aggregates were completely removed from the funnel walls at a low flow rate (10μl/min) within 7min., while sucrose-dependent aggregates were removed from the walls only at higher flow rates (25 and 50μl/min) within several minutes. These results suggest that sucrose-dependent aggregates are more tolerant of shear stress than sucrose-independent aggregates, and are more likely to remain in the region with the smallest shear stress in the teeth.