An endoscope system comprises an endoscope, a treatment instrument cartridge, an advancing and retracting device, a controlling device, and an operation instructing device. The endoscope includes a treatment instrument channel in an inserting portion. The treatment instrument cartridge includes a treatment instrument and a storage case. The treatment instrument includes a treatment instrument inserting portion having an elasticity which is inserted through the treatment instrument channel, a treatment section at the tip end thereof, and an operating portion at the base end thereof. The storage case includes an inserting portion storing section into which the treatment instrument inserting portion is wound, an extension port from which the tip end of the wound treatment instrument inserting portion is extended, and a holding section for holding the base end of the treatment instrument inserting portion or the operating portion. The advancing and retracting device has a driving power source and is provided between the treatment instrument inserting channel and the extension port. The controlling device is electrically connected to the driving power source and controls an operation of the driving power source. An operation instructing device issues an instruction on an operation of the driving power source to the controlling device.