All-optical logic gates with bacteriorhodopsin (W) protein molecules have been demonstrated based on all-optical switching of a cw probe laser beam by multiple pulsed pump laser beams due to nonlinear intensity-induced excited-state absorption. A cw probe laser beam at 640 nm corresponding to the peak absorption of O-state in the bR photocycle is switched by a pulsed pump laser beam at 570 nm corresponding to the maximum initial B state absorption, at relatively low powers. The switching characteristics have been used to design all-optical NOT and the universal NOR and NAND logic gates and the effect of various parameters such as variation in pump pulse width, pump intensity, lifetime of 0 state and absorption cross-section of the B state at probe wavelength on the switching characteristics has been analyzed. (C) 2002 Elsevier Science B.V. All rights reserved.