PROBLEM TO BE SOLVED: To provide an optical waveguide type measurement system in which detection sensitivity of a measurement object material is more improved to higher accuracy, and a measurement method and an optical waveguide type sensor chip thereof. SOLUTION: The optical waveguide type measurement system includes an optical waveguide having a sensing area where first substances that specifically bind to the measurement object material are immobilized; magnetic fine particles in which second substances that specifically bind to the measurement object material are immobilized, and which have magnetism; a magnetic field applying unit for generating a magnetic field that moves the magnetic particles; a light source that makes light incident to the optical waveguide; and a light receiving element for receiving light emitted from the optical waveguide. COPYRIGHT: (C)2013,JPO&INPIT