A pattern transfer apparatus includes a storage-medium-surface detecting unit that detects a foreign substance or defect on a surface of a storage medium and specifies a position and a size of the foreign substance or defect; a relative-position adjusting unit that adjusts a relative position on a contact surface between the surface of the storage medium and a transfer pattern surface of a transfer master, and a relative-position-adjustment instructing unit that calculates an adjusted value of the relative position according to a detection result, and instructs the relative-position adjusting unit to adjust the relative position based on the adjusted value.