Provided are a magnetic disk substrate and a method of manufacturing the same, wherein the magnetic disk substrate has very few defects present on its surface with an arithmetic mean roughness (Ra) at a level in the vicinity of 0.1 nm and thus is suitable as a substrate for a magnetic disk with high recording density. The magnetic disk glass substrate is such that the arithmetic mean roughness (Ra) of the main surface of the glass substrate measured using an atomic force microscope with a resolution of 256×256 pixels in a 2 μm×2 μm square is 0.12 nm or less and the number of defects detected to have a size of 0.1 μm to 0.6 μm in plan view and a depth of 0.5 nm to 2 nm is less than 10 per 24 cm2, wherein the defects are each detected using a shift in wavelength between incident light and reflected light upon irradiating and scanning helium neon laser light with a wavelength of 632 nm on the main surface of the glass substrate.