Systems and methods are provided for performing a surgical procedure on a beating heart of a patient. Methods are provided which include positioning an end effector in close proximity to a surgical site on the heart, the end effector being mounted on a robotically controlled arm. The motion of the surgical site is monitored and end effector tracking command signals computed in response to the monitored motion of the surgical site. The tracking command signals are forwarded to actuators operatively associated with the robotically controlled arm to cause the arm to move the end effector generally to track motion of the surgical site. The method further includes inputting an end effector movement command signal, and forwarding the end effector movement command signal to the actuators to cause the end effector to move relative to the surgical site so as to perform at least part of the surgical procedure.