Deformation of each cell, as it passes through the micro-slit in the flow channel, has been investigated in vitro. A slit with a rectangular cross section (height 10 μm, width 0.4 mm, length 0.1 mm) was made in the center of the flow path by photolithography technique. Myoblasts (C2C12: mouse myoblast cell line) were used for the test. The flow rate of the medium, in which the cells were suspended, was controlled by a pressure head between the inlet and the outlet. Deformation of each cell passing through the micro-slit was observed with an inverted phase contrast microscope. Using the contour of the image of each cell passing through the slit intermittently, several parameters were analyzed: the two-dimensional projected area, the degree of deformation by ellipse approximation, and the deformation direction. The experimental results show that elongation of the cell in the slit tends to decrease the area of the cell.