An observation device comprising: a stage on which a plurality of containers in which an observation target is contained are placed; an imaging optical system that includes an objective lens for forming an image of the observation target in each container; a horizontal driving section that moves at least one of the stage or the imaging optical system in a horizontal plane; a scanning controller that controls the horizontal driving section to move at least one of the stage or the imaging optical system, to scan an observation position in the stage; an imaging optical system driving section that moves the objective lens in an optical axis direction; an auto-focus controller that controls the imaging optical system driving section to perform an auto-focus control at each observation position; and a detection section that precedently detects a vertical position of the container placed on the stage at the observation position before the imaging optical system reaches the observation position, wherein the auto-focus controller performs the auto-focus control at the observation position on the basis of a detection signal of the detection section, wherein the auto-focus controller starts the auto-focus control at an observation position just behind a boundary portion between the containers that are adjacent to each other in a scanning direction, after a time point when the auto-focus control at an observation position just in front of the boundary portion is terminated and before the imaging optical system reaches the observation position just behind the boundary portion, and wherein the auto-focus controller starts the auto-focus control at a different observation position (R0, R1, R3) other than the observation position just behind the boundary portion, from a time point when the imaging optical system reaches the different observation position (R0, R1, R3). a stage on which a plurality of containers in which an observation target is contained are placed; an imaging optical system that includes an objective lens for forming an image of the observation target in each container; a horizontal driving section that moves at least one of the stage or the imaging optical system in a horizontal plane; a scanning controller that controls the horizontal driving section to move at least one of the stage or the imaging optical system, to scan an observation position in the stage; an imaging optical system driving section that moves the objective lens in an optical axis direction; an auto-focus controller that controls the imaging optical system driving section to perform an auto-focus control at each observation position; and a detection section that precedently detects a vertical position of the container placed on the stage at the observation position before the imaging optical system reaches the observation position, wherein the auto-focus controller performs the auto-focus control at the observation position on the basis of a detection signal of the detection section, wherein the auto-focus controller starts the auto-focus control at an observation position just behind a boundary portion between the containers that are adjacent to each other in a scanning direction, after a time point when the auto-focus control at an observation position just in front of the boundary portion is terminated and before the imaging optical system reaches the observation position just behind the boundary portion, and wherein the auto-focus controller starts the auto-focus control at a different observation position (R0, R1, R3) other than the observation position just behind the boundary portion, from a time point when the imaging optical system reaches the different observation position (R0, R1, R3).