A microgap was created in the flow channel, and the behavior (deformation, rotation) of each cell when passing through the gap was investigated. A gap with a rectangular cross section (7 μm high, 0.4 mm wide, and 0.1 mm long) was manufactured in the middle part of the flow path by photolithography technique. Myoblasts (C2C12: mouse myoblast cell line) sparsely suspended in the medium were used for the test. Deformation of each cell passing through the microgap was observed with an inverted phase contrast microscope. From the contour of the image of each cell passing through the gap, several parameters were analyzed: the two-dimensional projected area, the degree of deformation by ellipse approximation, and the alignment of the major axis of the deformed cell. The experimental results show that the alignment of each cell tends to deviate from the flow direction as the larger projected two-dimensional area pressed in the gap.