Approximately 60% of VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula with atresia, renal defects/radial limb dysplasia) patients have renal anomalies that can be associated with chronic kidney disease (CKD). With improved medical care, a large proportion of these patients survive into adulthood. Longitudinal follow-up data regarding the management of kidney disease in these children is lacking. Twelve VACTERL patients with CKD stage 2–5 and 12 age-matched controls with similar urologic anomalies and CKD [mean follow-up period 15.0 ± 1.4 (SE) and 11.9 ± 2.1 years, respectively] were identified in a single center. Eight VACTERL patients progressed to end-stage renal disease (ESRD) compared to four controls (66.7 vs. 33.3%, respectively). Six VACTERL patients were dialyzed pre-transplant. Of the four patients on peritoneal dialysis (PD), three had to be switched to hemodialysis due to complications, whereas two of the three controls on PD did not experience significant problems. Seven VACTERL patients underwent renal transplantation compared to four controls. Mean creatinine clearance 2 years post-transplant was 65.8 ± 6.3 in VACTERL patients vs. 87.8 ± 7.1 ml/min per 1.73 m2 in controls (p = 0.03). VACTERL patients had a significantly lower mean height standard deviation score than the controls (−2.34 ± 0.41 vs. −1.27 ± 0.24, respectively; p < 0.05). Based on these results, VACTERL patients with CKD develop ESRD more frequently, experience more complications with dialysis, may have a poorer transplant outcome, and have more severe growth failure than controls.