A medical observation system, a control method, and a program are provided, which are capable of easily reducing the possibility that illumination light directly enters an eye by accident. A medical observation system 1 includes: an imaging unit 21 that captures an object and generates an image signal； a light output unit 22 that outputs illumination light in a capturing direction of the imaging unit 21； a determining unit 942 that determines the usage state of the imaging unit 21； and an illumination controller 944 that controls illumination light emitted by the light output unit 22 based on a determination result of the determining unit 942.
