Cardiovascular diseases (CVD), such as heart attacks and strokes, are the leading cause for mortality worldwide. Many studies have shown beneficial effects of physical exercise on cardiovascular risk factors, such as high cholesterol, high blood pressure, abdominal obesity and diabetes. However, some of the mechanisms, by which these beneficial effects occur, are not well understood. It is believed that gut microbiota, affected by physical exercise, altering the intestinal environment, plays a role. This review paper summarised the current understanding on the effects of physical exercise on CVD, through its effects on the gut microbiota and intestinal function. The authors reviewed animal and human studies looking at how various types of exercise, such as high-intensity interval training (mice), running (rats and mice) and rugby (humans), affect diversity and distribution of microbes, metabolites produced by microbiota, intestinal wall integrity and systemic inflammation. Based on the reviewed papers, the authors concluded that, although further research is warranted, many studies confirm the premise that physical exercise can prevent CVD through modifying gut microbiota and alleviating systemic inflammation.