An apparatus for measuring contamination of a semiconductor substrate includes a chuck for loading a substrate, a position detection means for recognizing a front surface of the loaded substrate to obtain position data of a portion of the substrate to be measured, a first driving part for moving the chuck in accordance with the position data to measure a rear portion of the substrate, and a surface measurement means disposed under the chuck for selectively measuring metal contamination of the substrate at the rear portion of the substrate. In operation, the substrate is loaded onto a chuck, position data of a portion of the substrate to be measured is obtained by recognizing patterns formed on the substrate, the substrate is then moved in accordance with the position data to measure a rear portion of the substrate, and metal contamination is selectively measured at the rear portion of the substrate.