The increased prevalence of morbid obesity is associated with an increased prevalence of obesity co-morbidities. Bariatric surgery is generally the only effective treatment. Gastric bypasses are the most common bariatric operation in many countries, and more than half are performed laparoscopically. We discuss the challenges encountered in performing laparoscopic gastric bypass and cholecystectomy in a morbidly obese patient who was found to have malrotated small and large bowel when the procedure started. In the absence of past gastrointestinal symptoms and investigations, there is no way of diagnosing this anomaly preoperatively. However, when such a problem is posed at the time of surgery, it is safe to perform the planned operation if the surgeon has experience and skills in advanced laparoscopic techniques.