Circadian expression, light-responsiveness and localization of clock genes, rPer1 and rPer2, were examined in the rat retina under constant darkness. A significant circadian variation was detected in rPer2 transcript levels with a peak at ZT14, but not in the rPer1. A light pulse given after constant darkness of 3 days increased both rPer1 and rPer2 expression phase-dependently, while rPer1 was induced at more times than rPer2. A major site of these gene expression within the retina was the inner nuclear layer. These findings indicate that rPer1 and rPer2 genes play different roles in the generation and regulation of circadian rhythms in the retina from those in the suprachiasmatic nucleus.