A scanning apparatus for transparent documents includes a scanner which includes a host and a lid pivotally coupled with the host, and a transparent document holding module which is located between the host and the lid, and includes a main body and a light guide element which is located on the periphery of the main body. The host has an optical module for scanning. The optical module includes a plurality of lighting units and a first attraction element. The main body aims to hold a transparent document. The light guide element includes a second attraction element attracted to the first attraction element. When the light guide element is moved with the optical module, the direction of light projecting to the transparent document is altered. Thus when the light guide element is moved with the optical module along a track, scanning of images on the transparent documents can also be accomplished.