The present specification discloses an automated method and apparatus useful for separating and harvesting cells of interest, e.g., mononuclear cells, in a whole blood sample. The method of the invention uses the aspirating/dispensing probe of an automated sample preparation instrument to underlay a density gradient medium beneath a whole blood sample in a centrifugation tube, and the same probe is used to harvest cells of interest from a cell layer formed in the tube as a result of a centrifugation step. In harvesting cells, the probe is advanced inside the tube by a fixed, predetermined distance at which the probe tip (i.e., its aspiration port) is known to be located at, or within a predetermined distance below, the bottom of the cell layer. A predetermined volume of liquid is then aspirated through the probe tip, whereby most cells of interest (and more than 90% of those cells that can be harvested by a flawless manual method) are removed from the cell layer and collected for analysis. Preferably, the probe is caused to move laterally with respect to the tube during the aspiration of the cell layer, whereby cells offset from the center of the container are readily harvested.