Previously, it was shown that milk fermented with lactic acid bacteria lowers blood pressure, suggesting that metabolites or components of the bacteria have hypotensive action. To examine whether one of lactobacilli, Lactobacillus johnsonii La1 (LJLa1), a probiotic strain adhesive onto intestinal epithelial cells, or its metabolite has hypotensive action, and if so the mechanism of action, we determined the effects of intraduodenal injection of LJLa1 on blood pressure (BP) and the activity of autonomic nerves in urethane-anesthetized rats. Intraduodenal injection of LJLa1 reduced renal sympathetic nerve activity (RSNA) and BP and enhanced gastric vagal nerve activity (GVNA). Pre-treatment with thioperamide, a histaminergic H3-receptor antagonist, eliminated the effects of LJLa1 on RSNA, GVNA, and BP. Furthermore, bilateral lesions of the hypothalamic suprachiasmatic nucleus (SCN), the master circadian oscillator, abolished the suppression of RSNA and BP and the elevation of GVNA caused by LJLa1. These findings suggest that LJLa1 or its metabolites might lower BP by changing autonomic neurotransmission via the central histaminergic nerves and the suprachiasmatic nucleus in rats.