An endoscope system comprises an endoscope (10), medical instrument, operating unit (45), first (40) and second (30) drive units, and control unit (20). The endoscope comprises a flexible insertion tube (11) being inserted into an object being examined. The medical instrument is partially inserted into the object through the insertion tube (11) and the operating unit (20) is used for commanding the medical instrument to operate. The first drive unit (40) drives the medical instrument to enable an inserting and pulling-out operation of the medical instrument with the object through the insertion tube (11). The second drive (30) unit drives the medical instrument to enable the medical instrument to perform a therapeutic operation in the object. The control unit (20) controls drive of the first and second driving devices depending on both an operated state of the operating device and an interference state caused between the medical instrument and the insertion tube when the instrument is actually used.
