Although an antihypertensive effect of fermented milk has been demonstrated in many human and animal experiments, the molecular mechanism controlling it is still poorly understood. In this study, we used DNA microarray analysis to determine the molecular mechanism of the antihypertensive effect of fermented milk. The results showed that gene expression in the left ventricle of spontaneously hypertensive rats was regulated when milk fermented by Lactobacillus helveticu s ( L. helveticus ) H9 was administered. Some hypertension-associated genes were differentially expressed. In-depth analysis showed that these differentially expressed genes were related to NO synthesis, cell proliferation, endothelin binding, and blood clot breakdown. These processes could be responsible for the antihypertensive response and relief of left ventricular hypertrophy observed. It is likely that regulation of the gene expression of endothelial nitric oxide synthase (eNOS), peroxisome proliferator-activated receptor γ (PPARγ), endothelin type A receptor (Ednra), and other hypertension-associated genes play an important role in these processes. In summary, this study provided valuable information that contributes to our understanding of the molecular mechanisms by which antihypertensive effects are provided from milk fermented by L. helveticus H9.