A surgical system includes an endoscope, a pair of end effectors provided on the outside of the distal end of a endoscope (“on-scope”), in which one end effector is rotatable or otherwise movable relative to the second end effector and in which such movement is effected via controls elements which do not extend through a lumen of the endoscope, and another instrument extending through the lumen of the endoscope (“through-scope”), and which preferably also has a pair of end effectors. The on-scope device may be clamping jaws, needle passers, clip appliers, cautery devices, staplers, and releasable hemoclips, among other end devices. The through-scope end effectors may be graspers and clip appliers, among other end effectors.