Permanent middle cerebral artery occlusion (MCAO) causes neuronal cell death in the striatum and cortex. In rodents, estradiol treatment protects the cortex from cell death in an estrogen receptor alpha (ERalpha) dependent manner. ERalpha is only transiently expressed in the cortex during neonatal development and is very low in uninjured adult cortex. Following MCAO, ERalpha mRNA expression is upregulated in the cortex of female rats, but the mechanism of this increase is still unknown. It is also unknown whether a similar increase in ERalpha expression in seen in males. In the following studies, male and vehicle or estradiol-treated ovariectomized (OVX) female rats underwent MCAO to investigate the regulation of ERalpha expression after ischemia. Twenty-four hours after surgery, mRNA or genomic DNA was collected from 1 mm micropunches taken from 300 mum brain sections for quantitative reverse transcription-polymerase chain reaction (RT-PCR) or methylation-specific (MSP) PCR, respectively. Additionally, adjacent 20 mum sections were processed for ERalpha immunohistochemistry. In OVX females, ERalpha mRNA and protein were increased in the ischemic cortex, but unchanged in males. We hypothesized that this increase in ERalpha in females is due to a reversal of gene silencing by DNA methylation. Using MSP targeting of CpG islands within the 5' untranslated region (UTR) of the rat ERalpha gene, we found that ischemia decreased methylation in the ischemic cortex of both groups of females, but there was no change in methylation in males. Using chromatin immunoprecipitation, we found that MeCP2 associates with ERalpha 5'UTR corresponding with the methylation status of the promoter. These data are the first to demonstrate a difference in the regulation of ERalpha expression in response to MCAO between males and females and that methylation of the ERalpha gene corresponds with mRNA levels in the brain.