Cardiovascular diseases are the most common causes of hospitalization, death, and disability in Europe. Due to high prevalence and ensuing clinical complications, they lead to very high social and economic costs. Despite the knowledge of classical cardiovascular risk factors, there is an urgent need for discovering new factors that may play a role in the development of cardiovascular diseases or potentially influence prognosis. Recently, particular attention has been drawn to the endogenous microflora of the human body, mostly those inhabiting the digestive system. It has been shown that bacteria, along with their host cells, create an interactive ecosystem of interdependencies and relationships. This interplay could influence both the metabolic homeostasis and the immune processes of the host, hence leading to cardiovascular disease development. In this review, we attempt to describe, in the context of cardiovascular risk factors, why particular microbes occur in individuals and how they might influence the host’s cardiovascular system in health and disease.