Apparatus of easily controlling the Z-position of the probe used in a microprobe analyzer. The apparatus has: (A) a holder, (B) a reference body having a reference surface that is at the same height as a surface of a sample, the reference body being placed on or in the holder, (C) a probe-positioning device for bringing the probe into contact with the reference surface, (D) a controller for controlling motion of the probe-positioning device in the Z-direction, (E) position-measuring apparatus for measuring the Z-coordinate of the probe at which it is in contact with the reference surface, (F) a memory for storing a positional coordinate outputted by the position-measuring apparatus, and (G) probe contact detection apparatus for detecting that the probe is in contact with the reference surface.