An analysis device comprising: an analysis substrate on which a plurality of reaction regions are formed, the reaction regions including a first region and a second region that are arranged in a checkered pattern so that the first region and the second region do not overlap each other, the first region being fixed with a first antibody that is specifically bound with a first detection target substance to be captured in the first region, and the second region being a region other than the first region in the reaction region and being fixed with a second antibody that is not specifically bound with the first detection target substance to be captured in the first region; an optical pickup configured to irradiate the analysis substrate with a laser beam and receives reflected light from the analysis substrate to generate a light reception level signal, the analysis substrate being bound with the first detection target substance which is reacted with the first region and the second region and being bound with a count target substance which is bound with the first detection target substance captured by the reaction; a signal processing circuit configured to extract a pulse signal indicating the count target substance from the light reception level signal, and counts a pulse number in the pulse signal; and a control unit configured to control the optical pickup so as to scan the analysis substrate; wherein the signal processing circuit is configured to generate a first gate signal corresponding to a time period for scanning the first region, and a second gate signal corresponding to a time period for scanning the second region, and comprises a first computation unit configured to calculate a first count value (Ca) in the first region based on the first gate signal and the pulse signal, and configured to calculate a second count value (Cb) in the second region based on the second gate signal and the pulse signal; the control unit comprises a second computation unit configured to calculate a relative count value (Rc) in the reaction region based on the first count value (Ca) and the second count value (Cb), and the first count value (Ca) is calculated by totaling count values in a plurality of the first regions, and the second count value (Cb) is calculated by totaling count values in a plurality of the second regions. an analysis substrate on which a plurality of reaction regions are formed, the reaction regions including a first region and a second region that are arranged in a checkered pattern so that the first region and the second region do not overlap each other, the first region being fixed with a first antibody that is specifically bound with a first detection target substance to be captured in the first region, and the second region being a region other than the first region in the reaction region and being fixed with a second antibody that is not specifically bound with the first detection target substance to be captured in the first region; an optical pickup configured to irradiate the analysis substrate with a laser beam and receives reflected light from the analysis substrate to generate a light reception level signal, the analysis substrate being bound with the first detection target substance which is reacted with the first region and the second region and being bound with a count target substance which is bound with the first detection target substance captured by the reaction; a signal processing circuit configured to extract a pulse signal indicating the count target substance from the light reception level signal, and counts a pulse number in the pulse signal; and a control unit configured to control the optical pickup so as to scan the analysis substrate; wherein the signal processing circuit is configured to generate a first gate signal corresponding to a time period for scanning the first region, and a second gate signal corresponding to a time period for scanning the second region, and comprises a first computation unit configured to calculate a first count value (Ca) in the first region based on the first gate signal and the pulse signal, and configured to calculate a second count value (Cb) in the second region based on the second gate signal and the pulse signal; the control unit comprises a second computation unit configured to calculate a relative count value (Rc) in the reaction region based on the first count value (Ca) and the second count value (Cb), and the first count value (Ca) is calculated by totaling count values in a plurality of the first regions, and the second count value (Cb) is calculated by totaling count values in a plurality of the second regions.