Obesity and its associated comorbidities have become one of the largest challenges for health care in the near future. Conservative therapy for obesity and related comorbidities has a very high failure rate and poor long-term results. Similarly, the conservative and medical management of the majority of metabolic diseases such as type 2 diabetes mellitus are only able to slow down disease progression but have no causal effect on the disease process. Obesity surgery has evolved as a highly effective therapy for severe obesity achieving long-lasting weight loss. Furthermore, several studies have demonstrated the beneficial effects of obesity surgery on reduction of overall mortality, reduction of cardiovascular events and superior control of obesity-related diseases such as type 2 diabetes mellitus, dyslipidemia and also the non-alcoholic steatohepatitis compared to medical therapy. Based on these findings, the term 'metabolic surgery' with the focus on treating metabolic diseases independent of body weight has been coined. Of great interest are recent studies that show that even existing complications of metabolic diseases such as diabetic nephropathy or the non-alcoholic steatohepatitis can be reversed by metabolic surgery. Although metabolic surgery has proven to be a safe and effective treatment for obesity, resolution of comorbidities and enhancing quality of life, it is still uncertain and unclear, which surgical procedure is the most effective to achieve these metabolic effects. The aim of this review is to compare the effects of the two currently most widely used metabolic operations, the Roux-en-Y gastric bypass and the sleeve gastrectomy in the treatment of obesity and its related comorbidities.