A magnetic sensor used to detect a detection target substance in a sample includes a substrate having a first surface and a second surface, which is opposite the first surface and a magnetoresistive effect element provided on the first surface of the substrate. The resistance of the magnetoresistive effect element changes in accordance with an input magnetic field. A protective layer covers the top of the magnetoresistive effect element. The surface of the protective layer, which is positioned on top of the magnetoresistive effect element, has a prescribed surface roughness.