An object is to provide a biological sample observation system wherein light damage to the biological sample is decreased, and observation can be performed accurately and quickly over a long period of time. A biological sample observation system which continuously obtains information on a biological sample that is cultured inside of a culturing container has: an imaging section which observes mutually different regions that are previously selected, among regions to be observed including the biological sample, through an object lens for observing the biological sample in the culturing container through a part of the culturing container; an autofocus section which detects the focusing of the object lens with respect to a predetermined region among the regions to be observed; and a focusing drive control section which controls the focusing of the object lens when the biological sample is observed using the imaging section, based on the detection result of the focusing previously performed by the autofocus section. After the focus detection is performed by the autofocus section, without being intervened by the focus detection using the autofocus section, and the different regions are continuously observed by the imaging section, with the focusing controlled by the focusing drive control section.
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