Obesity predisposes to cardiovascular risk factors such as dyslipidemia, type 2 diabetes, nonalcoholic fatty liver disease and hypertension. In contrast to the limited success of pharmacological and lifestyle interventions, RYGBP induces sustained weight loss, metabolic improvements and decreases morbidity/mortality. In line, RYGBP reduces cardiovascular risk factors. Although the mechanisms are not entirely understood, RYGBP induces complex changes in the gut affecting other organs through endocrine and metabolic signals from the intestine to all key metabolic organs, which can link RYGBP and decreased cardiovascular risk. Here, we discuss the roles of changes in lipid absorption and metabolism, bile acid metabolism, gut hormones and the microbiote as potential mechanisms in the decreased cardiovascular risk and metabolic improvement after RYGBP.