Surgical instruments having a rotary drive that can selectively actuate multiple end effector functions are described herein. In at least one embodiment, a surgical instrument includes an outer shaft, an end effector coupled to the outer shaft, a rotatable drive shaft coaxially disposed within an inner lumen of the outer shaft, and a plurality of selectively engageable clutches configured to transfer torque from the rotatable drive shaft to the end effector. The surgical instrument further comprises sensors configured to detect the engagement and/or disengagement of the clutches.