The prevalence of cardiovascular disease is a major public health concern worldwide. It has been theorized that diets rich in fruits and vegetables may be protective against the development of cardiovascular disease mainly through their high content of flavonoids. Flavonoids were thought to influence traditional risk factors of cardiovascular disease such as blood pressure, lipid profile, and systemic inflammation. Recent clinical studies have shown that this may not be the case. The production of trimethylamine oxide (TMAO) by the gut microbiota from dietary sources of choline has been associated with an increased risk of cardiovascular events. The objectives of this study were to determine the effects of a high flavonoid diet on gut microbiota composition and plasma trimethylamine oxide concentrations. Potential benefits of this research include the determination of a potential correlation between diet and markers of traditional and non-traditional risk factors for cardiovascular disease. Also, the effects that a high flavonoid diet has on the composition of the gut microbiota and plasma trimethylamine oxide concentrations may provide insight into possible dietary interventions to prevent cardiovascular disease.