Abstract Genetically mutant anophthalmic rats lacking a complete visual system due to the absence of eyeballs and optic nerves up to the optic chiasma were used as a model to study photo-regulated physiological activities. The photoreception in these mutant rats was determined by measuring the neuroendocrine response of the pineal gland-melatonin levels in the serum, and synaptic ribbon complexes (SRCs) in the pinealocytes. These parameters were studied in both normal and anophthalmic rats maintained under light–dark (LD 12:12), continuous dark (DD) and light (LL) conditions. Both normal and mutant anophthalmic animals showed nocturnal increases in serum melatonin levels and in the number and diameter of SRC and their vesicles in the pinealocytes in LD. The daily rhythms persisted even upon transfer to DD both in normal and mutant rats, whereas in LL, the nocturnal elevation of both the parameters disappeared. These observations suggested that congenitally blind rats can perceive light. The studies of these parameters in both normal and mutant rats in reversed-LD conditions confirmed that pineal rhythms can be entrained by light–dark cycles in congenitally anophthalmic mutant rats through a nonvisual system for light perception.