To investigate the molecular mechanism of the melatonin rhythm in the mammalian retina, we examined the temporal mRNA expression pattern of serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase, AA-NAT; the rate-limiting enzyme in melatonin synthesis) in the rat retina. Northern blot analysis showed that in a daily light-dark cycle retinal AA-NAT mRNA was low during the day and increased more than threefold at night, and this daily rhythm persisted even in constant darkness. These findings suggest that AA-NAT mRNA expression in the rat retina is regulated by an endogenous circadian clock.