Disclosed herein is a scanning probe microscope including a cantilever, a three-dimensional moving mechanism moving a sample stage in three dimensions, and a measurement chamber sealed not to be exposed to external air. At least the cantilever, the sample stage, and the three-dimensional moving mechanism are accommodated in the measurement chamber. The measurement chamber is provided with a pair of guide rails used to transport the sample stage. The sample stage has an engagement portion. The three-dimensional moving mechanism is disposed in the vicinity of a predetermined position and between the guide rails. The three-dimensional moving mechanism can be moved to above the guide rails and below the guide rails. When the sample stage is transported to the predetermined position in a horizontal direction, the three-dimensional moving mechanism is lifted up to the bottom surface of the sample stage so that the scanning probe microscope can perform measurement.