Caudal Duplication Syndrome is a rare case, congenital anomalies, involved the alimentary tract duplications and urogenital tracts duplication. The incidence is 1:100.000 births. We present a case of two months old female baby with abnormal genitalia and imperforate anus related to caudal duplication syndrome. On physical assessment we found duplication of vagina with single uterus and urethra with anorectal malformation (anovestibular and rectovaginal type). Intraoperative findings showed double-duplication of ascending colon, transverse, descending and half of sigmoid with duplication of the rest of sigmoid and rectum; left-sided rectum was adjacent to left vestibule and right-sided rectum adjacent to the right vagina; duplication of bladder and urethral duplication. On fourth, the reconstruction surgery was performed to correct digestive abnormality with Posterior Sagittal Anorectoplasy (PSARP) and separating duplication segment using stapler. Stapler was enough to separate duplication. Further reconstructive surgery were needed to achieve better gastrointestinal and genitourinary function outcome.