Objective: The gap junction protein connexin40 (Cx40) is crucially important in cardiovascular physiology as evident from Cx40-deficient mice which exhibit arterial hypertension, high renin activity, cardiac hypertrophy, and arteriolar dysfunction. Recently, in a genome-wide association study (GWAS) a single nucleotide polymorphism (SNP) within the intron of GJA5 was associated with left ventricular hypertrophy (LVH). Because LVH is one consequence of long-lasting hypertension and Cx40-deficient mice are substantially hypertensive we searched for functional polymorphisms in the Cx40 gene (GJA5) in humans to explain this genetic association. Methods: DNA from probands carrying this SNP on both alleles (n=120) was isolated and the GJA5 coding and promoter region sequenced. The promoter activity was quantified after cloning the promoter into a luciferase reporter system and transfection of this construct into HeLa cells. Results: Of the two exons of GJA5 only the second encodes for the protein. Sequencing of this region (1077 bp) in 120 probands did not reveal alterations. Upstream of this region, we identified two base pair changes (SNPs) in complete linkage disequilibrium (LD) in 13 of 26 studied patients. In contrast, these SNPs were retrieved in a control population only with an allele frequency of 4%. Moreover, four different nucleotide exchanges were identified in a single proband. Promoter activity was unaffected by the two SNPs, but decreased by 40% if the promoter region contained the other four SNPs. Conclusion: Although we did not identify nucleotide exchanges in the coding exon of GJA5 in selected probands, sequencing of the promoter region uncovered SNPs which led to changes in transcriptional activity. Further studies are required to prove cell-specific effects and probably functional consequences in affected humans.