To determine whether estrogen has an effect on clock genes in the suprachiasmatic nucleus (SCN), we examined the effect of estrogen on the expression of Cry1 and Cry2 mRNAs in the SCN of female rats. Ovariectomized rats were injected with 20 microg 17beta-estradiol at zeitgeber time (ZT) 6 and ZT 18 and killed 24 h after the treatment. Northern blot revealed that the expression of Cry2 mRNA was significantly decreased in the SCN of estrogen-treated rats at both time points [correction]. But estrogen did not affect Cry1 mRNA levels in the SCN at any ZT. These results suggested that Cry1 and Cry2 mRNAs in the SCN were differently regulated by estrogen.