The present invention provides a substrate aligning system which prevents particles or the like from attaching to a substrate such as a wafer used in the semiconductor manufacturing process, and adjusts the orientation of the substrate accurately within a short period of time. According to a substrate aligning system (A) as a preferred embodiment of the present invention, a plurality of rollers (220) push the peripheral portion of a wafer (W) from different directions to align the center of the wafer. While the center of the wafer is kept aligned by the rollers (220), the contacting portion (211) of an contacting member (210) contacts a chip (Wa) of the wafer (W). The contacting member (210) is then moved arcuately to rotate the wafer (W), thus adjusting the orientation of the wafer.