A method of assigning an auxiliary input device to control a surgical instrument (102,103) in a robotic surgical system, the method comprising: detecting which of a user's left and right hands is providing input to remotely control movement of the surgical instrument (102,103), wherein the detecting comprises at least one of: sensing a configuration of an input device the user's hand is operating, wherein the configuration of the input device comprises a configuration to accommodate operation by a user's left hand or a configuration to accommodate operation by a user's right hand; and sensing movement of one of the user's left and right hands; and automatically assigning control of an auxiliary function of a surgical instrument (102,103) to a first auxiliary input device selected from a plurality of auxiliary input devices if the user's left hand is detected to operate the input device, the first auxiliary input device being disposed in a left position relative to a second auxiliary input device of the plurality of auxiliary input devices, or automatically assigning control of the auxiliary function of the surgical instrument (102, 103) to a second auxiliary input device if the user's right hand is detected to operate the input device, the second auxiliary input device being disposed in a right position relative to the first auxiliary input device of the plurality of auxiliary input devices, wherein a frame of reference of the left position and the right position is relative to a user operating the input device. detecting which of a user's left and right hands is providing input to remotely control movement of the surgical instrument (102,103), wherein the detecting comprises at least one of: sensing a configuration of an input device the user's hand is operating, wherein the configuration of the input device comprises a configuration to accommodate operation by a user's left hand or a configuration to accommodate operation by a user's right hand; and sensing movement of one of the user's left and right hands; and automatically assigning control of an auxiliary function of a surgical instrument (102,103) to a first auxiliary input device selected from a plurality of auxiliary input devices if the user's left hand is detected to operate the input device, the first auxiliary input device being disposed in a left position relative to a second auxiliary input device of the plurality of auxiliary input devices, or automatically assigning control of the auxiliary function of the surgical instrument (102, 103) to a second auxiliary input device if the user's right hand is detected to operate the input device, the second auxiliary input device being disposed in a right position relative to the first auxiliary input device of the plurality of auxiliary input devices, sensing a configuration of an input device the user's hand is operating, wherein the configuration of the input device comprises a configuration to accommodate operation by a user's left hand or a configuration to accommodate operation by a user's right hand; and sensing movement of one of the user's left and right hands; and automatically assigning control of an auxiliary function of a surgical instrument (102,103) to a first auxiliary input device selected from a plurality of auxiliary input devices if the user's left hand is detected to operate the input device, the first auxiliary input device being disposed in a left position relative to a second auxiliary input device of the plurality of auxiliary input devices, or automatically assigning control of the auxiliary function of the surgical instrument (102, 103) to a second auxiliary input device if the user's right hand is detected to operate the input device, the second auxiliary input device being disposed in a right position relative to the first auxiliary input device of the plurality of auxiliary input devices, wherein a frame of reference of the left position and the right position is relative to a user operating the input device.