Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of end-stage renal disease (ESRD) in children. Approximately one third of children with CAKUT have lower urinary tract dysfunction (LUTD). This article highlights the important aspects that need to be considered in kidney transplantation of children with complex urogenital malformations. The paper reviews the existing literature regarding the evaluation, preparation, perioperative management, and follow-up of children with complex urogenital malformations and ESRD undergoing renal transplantation. Comprehensive diagnostics are required before any pediatric kidney transplantation. If LUTD is suspected, voiding cystourethrography and aurodynamic examination should be performed. Treatment of symptomatic vesicoureterorenal reflux and LUTD is mandatory prior to pediatric kidney transplantation. Following successful kidney transplantation of children with congenital urogenital malformations, lifelong follow-up is required. Regular reevaluations of the bladder by means of urodynamic examinations are necessary. In patients following bladder augmentation with intestinal segments or urinary diversions in childhood, regular endoscopic examinations of the urinary tract are recommended to rule out secondary malignancy. Treatment of children with complex urogenital malformations should be carried out in centers with appropriate expertise.