We present the case of a 6-year-old boy who had an omphalocele repaired at day 1 of life. He had a secundum atrial septal defect and an anomalous inferior vena cava of a type which has not been previously reported. Cine-MRI was a useful noninvasive tool for diagnosing the anomalous subaortic innominate vein and four immature vessels which make up the venous drainage systems of the lumbar region. The recognition of this malformation is important in planning and executing surgical repair or cardiac catheterization for postoperative patients with omphaloceles.