As the demand for obesity surgery grows, Roux-en-Y gastric bypass remains the most commonly performed procedure associated with low complication rates and good long-term co-morbidity resolution and weight loss. Marginal ulcers remain a cause of significant morbidity in medium and long term and are reported in every large series of this operation. Marginal ulceration is a complex problem with unclear aetiology and lack of clear consensus on its prevention and management. A clearer understanding of the available evidence regarding the prevention and treatment of marginal ulcers is needed to improve patient care. We propose an algorithm for management of patients with marginal ulcers based on the best available evidence in the literature.