Given the strong genetic contribution to blood pressure and left ventricular hypertrophy (LVH), and the influence of estrogen on these parameters, we hypothesized that polymorphisms in the estrogen receptor alpha (ERalpha) promoter may influence LVH. Three novel polymorphisms were identified upstream of the ERalpha alternatively spliced exon 1E, within sequence which demonstrated significant promoter activity in vitro. Demonstration of ERalpha E isoform expression in human ventricle by RT-PCR supported a possible functional role for the 1E novel polymorphisms in estrogen signaling in the heart. Indeed, G>A (-721 E) was significantly associated with LVH after controlling for systolic blood pressure and sex in a healthy population (n=74), contributing to 23% of interventricular septum (IVS) width variance (p<0.001) and 9.4% of left ventricular mass index (LVMI) variance (p=0.035). In a separate hypertensive cohort, male carriers of the A allele (n=8) had a 17% increase in IVS (95% CI: 6-28%) and a 19% increase in LVMI (3-34%) compared to GG homozygotes (n=84). We conclude that a novel polymorphism in the promoter of a cardiac mRNA splice isoform of ERalpha is associated with LVH.