We report here a rare case of caudal regression syndrome associated with an intraspinal arachnoid cyst. The patient was a 6-month-old baby girl with multicomplex congenital abnormalities: sacrococcygeal dysgenesis and ventral curvature, large terminal cyst (myelocystocele), spinal arachnoid cyst, cerebellar hypertrophy (suspected), high imperforate anus, partial dysgenesis of the large intestine, omphalocele, atresia of the vagina, bilateral incomplete ureter duplication, incomplete pseudoduplicated bladder and bilateral talipes equinovarus. We performed plastic repair of the myelocystocele and perineal lesion for caudal regression syndrome and partial removal of the cyst wall for the intraspinal arachnoid cyst. She has been well for 3 years postoperatively, and her mental development is normal.