Abstract To investigate the effect of shear stress direction on the direction of cell activity in a confluent layer, the migration and deformation of cells oriented parallel or perpendicular to the direction of the shear flow field were optically tracked in vitro. A Couette-type shear flow between parallel walls was formed between the lower stationary culture dish and the upper rotating disk. Shear stress (<2 Pa) was set by adjusting the rotational speed of the upper disk. Myoblasts (C2C12: mouse myoblast cell line) were cultured in an incubator equipped with an inverted phase-contrast microscope under continuous shear flow for 7 days until confluency. Deformation and migration of each cell were tracked in time-lapse images. Analysis of these images showed that cells deform and migrate along their major axis even at confluency (whether the major axis of the cell is parallel or perpendicular to the shear stress field). As a result, the orientation of the major axis of the cell remains parallel or perpendicular to the shear stress field. This observation may be used to improve the development of engineered muscle tissue.