Urethral duplication is a rare congenital anomaly of the lower urinary tract which includes a wide range of anatomical variations. Y-type urethral duplication, which represents 6-30% of all forms, describes the condition, in which a functional urethra is implanted in the rectum with dysplastic topic urethra within penis. We report a case of premature newborn boy with multiple congenital anomalies (long-gap esophageal atresia with tracheoesophageal fistula, atrial and ventricular septal defect) and II A2 Y-type of urethral duplication. Diagnosis and management as well as review of literature on this subject are presented.