In recent years increasing evidence suggests that commensal microbiota may play an important role in health and disease, including cerebrovascular disease. Gut microbes impact physiology, at least in part by metabolizing dietary factors and also host-derived substrates and then generating active compounds including toxins. The purpose of the current review is to highlight the complex interplay between microbiota, their metabolites and essential functions for human health ranging from regulation of the metabolism and the immune system to modulation of brain development and function. We also discuss the role of gut dysbiosis in cerebrovascular disease, specifically in acute and chronic stroke phases and the possible implication of intestinal microbiota in post-stroke cognitive impairment and dementia, and we identify potential therapeutic opportunities of targeting microbiota in this context.