Anorectal malformation is a disease with different subtypes and anatomical and functional multisystemic involvement that requires a unique approach in each age group. Anomalies associated with vertebral defects, anal atresia, cardiac defects, tracheo-esophageal fistula, renal anomalies, and limb abnormalities (VACTERL) association require detailed investigation and management. Beginning from the neonatal period, treatment is carried out with different surgical procedures. The clinical course of these patients may be associated with medical problems, accompanying congenital anomalies, perioperative management, or late sequelae. Constipation and fecal–urinary incontinence are the most common problems encountered in long-term follow-up. Renal failure is the most important cause of long-term mortality. In addition, these patients need to be under control until adulthood due to cardiological, spinal, genital, gynecological, and endocrine problems. In this follow-up, many pediatric disciplines such as neonatal intensive care, cardiology, nephrology, gastroenterology, and endocrinology cooperate with pediatric surgeons and pediatric urologists.