PURPOSE: The aim of this study was to compare the frequency and nature of VACTERL associations between children who underwent surgery for esophageal atresia/tracheoesophageal fistula (EA/TEF) and anorectal malformation (ARM). METHODS: We identified all children who underwent surgery for EA/TEF and/or ARM at hospitals participating in the Pediatric Health Information System (PHIS) database between 2004 and 2012. PHIS is an administrative database of free-standing children's hospitals managed by the Child Health Corporation of America (Overland Park, KS) that contains patient-level care data from 43 hospitals. The complete records of patients in this cohort were cross-referenced for diagnoses of vertebral, cardiac, renal and limb anomalies. RESULTS: 2689 children underwent repair of esophageal atresia. Mean gestational age was 36.5+/-3.2weeks and mean birth weight was 2536.0+/-758.7g. Associated VACTERL diagnoses included vertebral anomaly in 686 (25.5%), ARM in 312 (11.6%), congenital heart disease in 1588 (59.1%), renal disease in 587 (21.8%) and limb defect in 192 (7.1%). 899 (33.4%) had 3 or more anomalies and met criteria for a VACTERL diagnosis. 4962 children underwent repair of ARM. Mean gestational age was 37.4+/-2.7weeks and mean birth weight was 2895.2+/-765.1g. Associated VACTERL diagnoses included vertebral anomaly in 1562 (31.5%), congenital heart disease in 2007 (40.4%), EA/TEF in 348 (7.0%), renal disease in 1723 (34.7%) and limb defect in 359 (7.2%). 1795 (36.2%) had 3 or more anomalies and met criteria for a VACTERL diagnosis. CONCLUSION: VACTERL associations are relatively common in children with EA/TEF and ARM and occur in specific clusters, with cardiac disease more common in EA/TEF and spinal and renal/urinary anomalies more common in ARM.