An alignment method is provided in which a substrate including first and second layers is aligned in forming a second pattern in the second layer. The method includes storing first alignment measurement data to be used in alignment performed in forming a first pattern and a second alignment mark in the second layer, the first alignment measurement data obtained by measuring a first alignment mark provided in the first layer; obtaining second alignment measurement data by measuring the second alignment mark through a resist applied over the second layer; obtaining third alignment measurement data by measuring the first alignment mark through the resist; and performing alignment of the substrate in accordance with a first difference between the first and second alignment measurement data, or in accordance with the first difference and a second difference between the first and third alignment measurement data.