Obesity is a global public health problem associated with chronic excess body fat and numerous complications, such as type 2 diabetes and cardiovascular disease. Obesity treatment requires a comprehensive approach, including lifestyle modification, pharmacotherapy, and bariatric surgery. Among the medications used in recent years, GLP-1 analogues and dual GLP-1/GIP agonists have gained particular attention, demonstrating high efficacy in weight loss. The aim of this paper was to review the current literature and recommendations on the side effects and complications of obesity treatment. Particular attention was paid to gastrointestinal symptoms associated with incretin-based drug therapy, as well as the incidence of gallstones associated with weight loss. A descriptive summary of the main findings from the latest documents and the resulting recommendations was presented.