Abstract Background Information on physical and developmental outcomes of children with anatomical congenital anomalies (CAs) may indicate the need for early intervention and reduce impact on the child's life and parental burden. Methods From 1999 to 2003, 101 children with CA (76.5% of initial survivors) were seen 6-monthly in a tertiary children's hospital. Growth, neurologic outcome, mental and psychomotor development as determined with the Bayley Scales of Infant Development, and categorization of predictive sociodemographic and medical variables of the children were evaluated prospectively and longitudinally. Results Congenital diaphragmatic hernia (CDH) and esophageal atresia patients showed impaired growth, that is, both height for age (−1.5 standard deviation score [SDS]) and weight for height (−1.0 SDS). Overall neurologic outcome was normal, however, suspect or abnormal for 40% of CDH patients. Overall mental development was normal, but psychomotor scores were significantly lower than the norm (95% confidence interval, 83.8-92.2 at 6 months and 87.9-98.5 at 24 months). Sex, maternal age, socioeconomic status, CA, severity-of-disease covariables, and need of medical appliances at home could predict negative outcome significantly ( P < .05). Conclusions The CA survivors show impaired growth and psychomotor developmental delay up to age 2 years. This warrants specific follow-up programs and infrastructure for these patients.