As the incidence of early gastric cancer increases, laparoscopic surgery has become one of the treatments of choice for gastric cancer. With the increase of laparoscopic surgery, the chance of discovering aberrant anatomy during the operation also increases. We present a case of laparoscopic total gastrectomy in gastric cancer patients with intestinal malrotation. Intestinal malrotation occurs in one in every 500 births. We found that laparoscopic total gastrectomy in such patients can be performed successfully when it is performed with a proper Roux limb orientation through an alternative minilaparotomy.