An apparatus for transporting substrates and a guide unit are disclosed herein. A guide unit can prevent a substrate from shaking in a side direction when the substrate is transported by the rotation of a transporting roller. The guide unit includes an inner ring and an outer ring. The outer ring includes a ring-shaped guide protruding from an outer circumferential surface of the outer ring in a side direction. The outer circumferential surface of the outer ring comes in contact with the bottom edge of a substrate to support the substrate, and a side surface of the guide comes in contact with the side of the substrate to prevent the substrate from traveling in a side direction. The inner ring rotates with the shaft, and the outer ring rotates by a friction force with the substrate.