This invention provides a magnetic sensor element that can detect a detection target substance with high accuracy. The magnetic sensor element includes a multi-magnetic domain structure in which a plurality of magnetic domains extend in a row in one direction and in which the magnetic domains that are adjoining have easy magnetization axes in opposite directions to each other. The multi-magnetic domain structure has a surface region. Within the surface region, when counting from one end of the multi-magnetic domain structure, affinities for a magnetic particle or a substance that can be immobilized on the magnetic particle are mutually different at a first surface portion located at a boundary between a (2n−1)th (n is a natural number) magnetic domain and a (2n)th magnetic domain and a second surface portion located at a boundary between the (2n)th magnetic domain and a (2n+1)th magnetic domain.