We developed the dual-micropillar-based microfluidic platform to direct embryonic stem (ES) cell fate. 4 × 4 dual-micropillar-based microfluidic platform consisted of 16 circular-shaped outer micropillars and 8 saddle-shaped inner micropillars in which single ES cells were cultured. We hypothesized that dual-micropillar arrays would play an important role in controlling the shear stress and cell docking. Circular-shaped outer micropillars minimized the shear stress, whereas saddle-shaped innermicropillars allowed for docking of individual ES cells. We observed the effect of saddle-shaped inner micropillars on cell docking in response to hydrodynamic resistance. We also demonstrated that ES cells cultured for 6 days within the dual-micropillar-based microfluidic platform differentiated into neural-like cells. Therefore, this dual-micropillar-based microfluidic platform could be a potentially powerful method for screening of lineage commitments of single ES cells.