A substrate inspection apparatus for inspecting a substrate having an irregular concave-convex surface for scattering lights, comprises a first irradiation system which irradiates the substrate with a first detection light; a first detection system which detects any luminance unevenness from the entire concave-convex surface of the substrate irradiated with the first detection light; a second irradiation system which irradiates the substrate with a second detection light having a wavelength different from that of the first detection light; and a second detection system which detects any defect of the concave-convex surface of the substrate irradiated with the second detection light. The luminance unevenness and a pattern defect of the substrate having the irregular concave-convex surface can be inspected effectively at low cost.