According to one embodiment, a cell identification system includes an imaging device and an identification device. The imaging device includes a well plate, a rotation mechanism, and an imaging part. The well plate is provided with a plurality of wells capable of accommodating cells. The rotation mechanism rotates the cells. The imaging part images the cells. The identification device includes processing circuitry. The processing circuitry controls the rotation mechanism to rotate the cells, controls the imaging part to image the cells each time the cells are rotated by the rotation mechanism, and inputs an image for the cells captured by the imaging part to a learned model so as to identify a cell in a good state from among the cells.