Flow-induced mechanical stress affects morphology of endothelial cells. The morphological remodeling of the cells is adaptive response by the mechanical stimulus. To address the mechanisms for the response, it is necessary to examine how the mechanical environment influences the adaptation process. Therefore, we tracked the same group of cultured endothelial cells during flow exposure, and measured surface geometry of the cells by confocal laser scanning microscopy. Flow field near the measured cell surface was then simulated by computational fluid dynamics, and the shear stress distribution on the cell surface was determined. When the cells, which were polygonal without alignment at the beginning of the flow exposure, elongated and aligned with the flow direction, mean shear stress of the cell group was decreased with time course. However, there were some cells on which mean shear stress per cell was increased, and morphological change of each cell was not always adaptive. The results show importance of interaction with surrounding cells for the adaptive response as cell layer.