Studies on neurodevelopmental outcomes in individuals with congenital anomalies who undergo neonatal surgery are scarce and have reported contradictory findings based on small study groups. The congenital condition VACTERL association includes at least three malformations: vertebral anomalies, anorectal malformations, cardiac defects, tracheoesophageal fistula with or without esophageal atresia, renal anomalies and limb deformities. Most of these patients undergo surgery during their first days of life. Neurodevelopmental disorders include a broad group of disabilities involving some form of disruption to brain development. Attention deficit hyperactivity disorder (ADHD), autism spectrum disorders (ASD) and intellectual disability (ID) are diagnoses included in this group. The aim of the study was to investigate the risk of ADHD, ASD and ID in a cohort of individuals with VACTERL association. Data was obtained from four Swedish national health registers and analyzed using the Cox proportional hazards model. Patients born 1973-2018 in Sweden with the diagnosis of VACTERL association were included in the study. For each case five healthy controls matched for sex, gestational age at birth, birth year and birth county were obtained. The study included 136 individuals with VACTERL association and 680 controls. Individuals with VACTERL had significantly higher risk of ADHD, ASD and ID than the controls; 2.25 (95% CI, 1.03-4.91), 5.15 (95% CI, 1.93-13.72) and 8.13 (95% CI, 2.66-24.87) times respectively. A higher risk of ADHD, ASD and ID was found among individuals with VACTERL association compared to controls. These results are of importance to caregivers and to professionals participating in follow ups of these patients in providing early diagnosis and support, aiming to optimize the quality of life of these patients.