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It has been proven a close relationship between intestinal microbiota and hypertension. Valsartan is a widely used ARB antihypertensive drug; so far, the effect of valsartan on intestinal microbiota remains largely unexplored. Herein, we evaluated the composition, structure and metabolites of intestinal microbiota of spontaneously hypertensive rats (SHRs) after valsartan administration. In the present study, valsartan administration decreased intestinal microbiota diversity, altered gut microbiota composition, leading to 192 unique OTUs deficiency ( vs WKY rats) and 10 unique OTUs deficiency ( vs SHRs) and did not prove impaired intestinal mucosal barriers. Valsartan decreased the production of isobutyric acid and isovaleric acid in SCFAs. Our findings revealed valsartan administration induced far-reaching and robust changes to the intestinal microbiota of SHRs and provided a better understanding of the relationship between efficacy of valsartan and gastrointestinal tract reaction.