A scanning microscope comprising: a light source that is adapted to emit illumination light, a scanner that is adapted to scan the illumination light from the light source in a two-dimensional direction crossing to a light axis, an objective lens that is adapted to irradiate the illumination light scanned by the scanner to a sample, and collect return light from the sample, a focusing position adjustment section that is adapted to adjust a focal position in a light axis direction of the objective lens, a light detector that is adapted to detect the return light collected by the objective lens, a storage section that is adapted to store intensity of the return light detected by the light detector, and positional information of an irradiating position of the illumination light set by the scanner and the focusing position adjustment section while relating the intensity to the positional information, an image processing section that is adapted to form a plurality of two-dimensional images parallel to the light axis on the basis of the intensity of the return light and the positional information of the irradiating position stored in the storage section with a time interval, a controller that is adapted to control the focusing position adjustment section and the scanner, wherein the scanning microscope is characterized in that the image processing section is adapted to further process the two-dimensional images so as to detect a moving distance along the light axis direction of a pointed area of the sample and to process the two-dimensional images so as to detect a moving distance of a horizontal direction of a pointed area of the sample, and the controller is adapted to control the focusing position adjustment section so as to correct a light condensing position of the illumination light and is adapted to control the scanner so as to correct a scan area in accordance with the moving distance of the pointed area detected by the image processing section. a light source that is adapted to emit illumination light, a scanner that is adapted to scan the illumination light from the light source in a two-dimensional direction crossing to a light axis, an objective lens that is adapted to irradiate the illumination light scanned by the scanner to a sample, and collect return light from the sample, a focusing position adjustment section that is adapted to adjust a focal position in a light axis direction of the objective lens, a light detector that is adapted to detect the return light collected by the objective lens, a storage section that is adapted to store intensity of the return light detected by the light detector, and positional information of an irradiating position of the illumination light set by the scanner and the focusing position adjustment section while relating the intensity to the positional information, an image processing section that is adapted to form a plurality of two-dimensional images parallel to the light axis on the basis of the intensity of the return light and the positional information of the irradiating position stored in the storage section with a time interval, a controller that is adapted to control the focusing position adjustment section and the scanner, wherein the scanning microscope is characterized in that the image processing section is adapted to further process the two-dimensional images so as to detect a moving distance along the light axis direction of a pointed area of the sample and to process the two-dimensional images so as to detect a moving distance of a horizontal direction of a pointed area of the sample, and the controller is adapted to control the focusing position adjustment section so as to correct a light condensing position of the illumination light and is adapted to control the scanner so as to correct a scan area in accordance with the moving distance of the pointed area detected by the image processing section.