In recent years, significant findings with respect to the association of the gut microbiota and various human diseases have been discovered. The diversity can be explained by a multitude of interactions between intrinsic and environmental factors that are unique to each individual. This uniqueness of the microbiota may explain why some individuals are more prone to develop cardiovascular diseases. Gut dysbiosis plays a significant role in various pathophysiological processes. It can be postulated that health is linked to the homeostasis of the gastrointestinal microbiota. We provide an overview of diagnostic procedures to determine the microbiota’s composition, the mechanisms of microbiota interactions and some effects of the microbiota on the development of cardiovascular diseases.