Aim: The aim of this study was to evaluate cognitive and motor development in children with major congenital anomalies and the predictability of development at age 5 years. Method: A prospective, longitudinal follow-up study was undertaken. The Dutch version of the Bayley Scales of Infant Development--Mental Developmental Index (MDI) and Psychomotor Developmental Index (PDI)--were administered at the ages of 6, 12, and 24 months. The Revised Amsterdam Children's Intelligence Test-IQ and the Movement Assessment Battery for Children-Total impairment score (TIS) were used at age 5 years. A total of 117 children participated in the study. After excluding 12 children who had a major chromosomal or syndromal abnormality, the analysis was limited to 105 children (50 females, 55 males). Seven groups of congenital anomalies were distinguished: (1) small intestinal anomalies; (2) abdominal wall defects, comprising gastroschisis and omphalocele; (3) oesophageal atresia; (4) congenital diaphragmatic hernia; (5) Hirschsprung disease; (6) anorectal malformations; and (7) miscellaneous diagnoses. Logistic regression analyses served to determine the ability of MDI and PDI to predict IQ and TIS at age 5 years. Results: At age five, 83.7% of 104 children had an IQ of 85 or above and 16.3% an IQ of less than 85. TIS was normal in 71.3% of 87 children, while 17.2% demonstrated a borderline score and 11.5% a definite motor problem. MDI and PDI scores showed equal sensitivity to predict IQ (p = 0.004 at 6 and 12mo, p = 0.001 at 24mo) and TIS (p less than 0.001 at 6 and 12mo, p = 0.002 at 24mo). MDI and PDI were positively correlated with IQ and TIS; TIS was positively correlated with IQ. Interpretation: IQ scores at 5 years of age corresponded to Dutch population scores, but TIS scores differed significantly. Early development of children with major congenital anomalies is predictive of development at 5 years, which can guide individualized follow-up for this vulnerable group of children.