Intestinal malrotation results from failure of intestinal rotation and fixation during fetal life. We report two cases of esophageal reconstruction with free jejunal flaps following total laryngopharyngectomy of hypopharyngeal and cervical esophageal carcinoma in which intestinal malrotation was detected during the jejunal flap harvesting. In both cases, the ligament of Treitz was absent, and the laparotomy incision was thus extended to identify the jejunum. In case 1, harvesting an adequate length of the vascular pedicle of the flap was impossible because of the abnormal position of the pancreas; thus, a jejunal flap of maximal length was harvested for optimal pedicle positioning in the recipient site. In case 2, Ladd's ligament prohibited the release of the jejunum from the ascending colon and required its dissection. Both patients underwent successful reconstruction. When the ligament of Treitz is absent during jejunal flap harvesting, investing the whole bowel by extended laparotomy incision is recommended. When anatomical abnormality caused by intestinal malrotation is detected, releasing an adhesion of the jejunum from circumferential organs and identifying the adequate vascular pedicle of a jejunal flap are necessary. If harvesting the long vascular pedicle is impossible, a jejunal flap of maximal length should be harvested for optimal positioning for vascular anastomosis at the shortest distance in the recipient site.