An analysis apparatus including a stage, an analysis device placed on the stage and including receiving sections which accommodate a sample and a reagent for biochemical reaction, and are communicated with one another through a flow path having an inlet and an outlet, a liquid introduction section which is connected to the inlet and supplies into the flow path the sample, the reagent, and an sealing liquid for sealing each of the receiving sections, and a waste liquid storage section which is connected to the outlet and stores as waste liquid an excess of the sample and the reagent and a part of the sealing liquid supplied to the flow path, an optical system which includes an objective lens, emits excitation light to the receiving sections and allows observation of fluorescence generated in the receiving sections by the excitation light, and a control unit that controls such that the sealing liquid and the excess of the sample and the reagent form an interface in the waste liquid storage section, and that the interface is formed at a distance not less than a fluorescence-obtainable distance from a bottom of the receiving sections.