PurposeAlthough congenital anomalies of the kidney and urinary tract (CAKUT) are among the leading causes of end-stage kidney disease (ESKD) in children and young adults, kidney transplantation access for this population has not been well studied in the US. We compared transplantation access in the US based on whether the etiology of kidney disease was secondary to CAKUT, and additionally by CAKUT subgroups (anatomic vs. inherited causes of CAKUT).MethodsUsing the United States Renal Data System, we conducted a retrospective cohort study of 80,531 children and young adults who started dialysis between 1995 and 2015. We used adjusted Cox models to examine the association between etiology of kidney disease (CAKUT vs. non-CAKUT, anatomic vs. inherited) and receipt of kidney transplantation, and secondarily, receipt of a living vs. deceased donor kidney transplant.ResultsOverall, we found an increased likelihood of kidney transplantation access for participants with CAKUT compared to those without CAKUT (HR 1.23; 95% CI 1.20–1.27). Among the subset of individuals with CAKUT as the attributed cause of ESKD, we found a lower likelihood of kidney transplantation in those with anatomic causes of CAKUT compared to those with inherited causes of CAKUT (adjusted HR 0.85; 0.81–0.90).ConclusionThere are notable disparities in kidney transplantation rates among CAKUT subgroups. Those with anatomic causes of CAKUT started on dialysis have significantly reduced access to kidney transplantations compared to individuals with inherited causes of CAKUT who were initiated on dialysis. Further studies are needed to understand barriers to transplantation access in this population.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11255-022-03459-z.