Nowadays, renal transplantation (RTx) is the best renal replacement therapy for children with end stage renal disease (ESRD) with the best survival. However, RTx in children is more challenging than adults with differences in many aspects including the etiology, the low circulatory volume and the more difficult maintenance of the extracellular fluid volume. In many instances, the native kidneys express a significant risk to the future renal graft. Consequently, native nephrectomy (NN) is indicated in these cases. This will be associated with more challenges related to the fluid management and nutrition in these children. This article will review the issue of NN in relation to pediatric RTx including its indications, its subsequent effect in children prepared for RTx, the proper timing for NN and precautions.The most common indications for NN are the presence of recurrent urinary tract infection (UTI) or proteinuria. Most of the diseases associated with these indications are more in children when compared with adults with ESRD due to the higher incidence of urologic anomalies and glomerulopathies. Although NN is associated with a reduction of the risk to the future renal graft as regard UTI and renal perfusion, it must be done with certain precautions to avoid any hazards to the child especially the risks resulting from loss of native urine production. Thus, timing of NN is very critical especially when bilateral NN is indicated. Medical treatment should be tried at first and if the condition is still refractory to treatment, a unilateral NN may be tried initially to keep at least one kidney as possible. Preservation of the native ureter is sometimes vital for the future possible ureteroureteral anasomosis or ureterocystoplasty particularly when facing post RTx ureteric complications.