A cell analysis apparatus including: a cell image acquisition unit that acquires an image of cells in a culture vessel in which cells are cultured; a smoothing processing unit that smooths luminance values in the image acquired by the cell image acquisition unit; a minimum-value detecting unit that detects minimum values of the luminance values smoothed by the smoothing processing unit; a smallest-minimum-value extracting unit that extracts smallest minimum values which are the smallest in regions according to the sizes of the cells, from the minimum values detected by the minimum-value detecting unit; a counting unit that counts the number of smallest minimum values extracted by the smallest-minimum-value extracting unit; and a cell-count calculating unit that calculates the number of cells in the culture vessel on the basis of the number of smallest minimum values counted by the counting unit.