Background The family of aquaporin water channels contributes to water and salt homeostasis. AQP5 is a ubiquitously expressed exocrine-type water channel. Functional single nucleotide polymorphisms in AQP5 which alter gene transcription have not yet been described. We, therefore, sequenced the human AQP5 promoter to detect novel sequence variants which could impact upon AQP5 expression and contribute to the phenotypic variability of the renin-angiotensin-aldosterone system (RAAS). Method and results Sequencing of the whole AQP5 promoter revealed a novel-1364A/C polymorphism. Substitution of C for A was associated with increased transcription factor binding as tested by electrophoretic mobility shift assay, but significantly reduced transcriptional activation of the AQP5 gene by cAMP and serum. The C allele was associated with significantly decreased mRNA in human heart and with decreased protein expression in erythrocyte membranes. Finally, we associated AQP5 genotypes with the variability of the RAAS in two independent study cohorts. First, we studied the phenotypic variability of the RAAS in 103 young (26 ± 3 years) healthy males under an increased dietary salt intake. Increasing salt intake decreased plasma angiotensin II by 25% in AC/CC genotypes but only by 2% in AA genotypes (P = 0.012), and it decreased serum aldosterone by 34% in subjects with AC/CC genotypes but only by 19% in the AA genotypes (P = 0.005). Both genotypes had increased blood pressure under salt diet (P < 0.01), which was significantly more pronounced in AA genotypes (P = 0.029). Second, we investigated associations with variables of the RAAS in 96 old patients (68 ± 10 years) with coronary artery disease scheduled for coronary artery bypass grafting. Aldosterone serum concentrations were 2-fold (P < 0.001) and angiotensin II plasma concentrations were 4-fold higher in AA genotypes than in AC/CC genotypes while ADH plasma concentrations did not differ. Conclusion A novel single nucleotide polymorphism in the AQP5 gene promoter alters AQP5 expression in different in vitro systems and cells, and is associated with alterations of variables of the RAAS both in young healthy males and in patients with coronary artery disease.