The site (intraocular vs. extraocular) of the biological clock driving a rhythm in melatonin content in the eyes of Japanese quail was investigated by alternately patching the left and right eyes of individual birds, otherwise held in constant light, for 12-hr periods. This patching protocol, therefore, exposed each eye to a light-dark cycle (LD 12:12) 180 degrees (12 hr) out of phase with the LD cycle experienced by the other eye. The optic nerves to both eyes were transected prior to initiating the patching protocol. The ocular melatonin rhythm (OMR) of the left eyes of quail could be entrained by this procedure 180 degrees out of phase with the rhythm expressed by the right eyes. Since optic nerve section would have deprived any putative extraocular clocks of photic entrainment information, the results show conclusively that the clock driving the OMR is located within the eye itself. In addition, the OMR of Japanese quail is remarkably unaffected by removing two potential neural inputs to the eye (sympathetic innervation from the superior cervical ganglia, and input from the isthmo-optic nucleus of the midbrain); this suggests that these inputs are not required to maintain the OMR. Finally, the clock driving the OMR of one eye does not appear to be coupled to the clock driving the OMR in the other eye, since permanently patching one eye abolished the ability of the patched eye to re-entrain to an 8-hr shift in the phase of an LD 12:12 cycle, whereas the exposed eye rapidly re-entrained to the phase-shifted cycle.