A medical system includes: a treatment tool including a treatment portion configured to treat a living body, a joint portion configured to move the treatment portion, a first indicator portion provided to correspond to a position of the joint portion, a sheath portion connected to the joint portion, and a driving portion connected to the sheath portion and configured to displace the joint portion; an overtube including a flexible tube portion having a distal end and a proximal end and holding the treatment tool such that the treatment portion is capable of protruding from the distal end, and a second indicator portion provided at the flexible tube portion to identify a predefined space where calibration of the treatment tool is performed; and a calibration mechanism configured to calibrate the treatment tool when the first and second indicator portions have a predetermined positional relationship.