To investigate the molecular mechanism of the melatonin rhythm in the mammalian retina, we examined the temporal mRNA expression pattern of arylalkylamine (serotonin) N-acetyltransferase (AA-NAT), the rate-limiting enzyme in melatonin synthesis in the rat retina. Rat AA-NAT mRNA was detected exclusively in the retinal photoreceptors in the outer nuclear layer-low during the day and increased more than threefold at night. The nocturnal AA-NAT expression in rat retina was also confirmed by RNase protection and the AA-NAT enzymatic activity. This is the first report to localize the site of AA-NAT mRNA circadian expression in mammalian photoreceptor cells. (C) 1998 Academic Press.