This case report describes a rare combination of anomalies in a female newborn with Down syndrome that included jejunal atresia, colonic atresia, and imperforate anus. The newborn underwent surgery including jejunal, duodenal, and colon resection and anastomosis with appendectomy and colostomy. However, the newborn did not survive due to postoperative cardio-respiratory arrest from pulmonary hemorrhage. This combination of multiple intestinal atresias with imperforate anus in a female newborn with Down syndrome represents an extremely rare presentation.