In 2 to 3% of newborns a congenital anomaly is detected. About 20% of these have even multiple anomalies. After a short review on the classification of congenital anomalies a description of the diagnostic workup is given with emphasis on items which are different from the usual clinical practice: pregnancy history, family history, dysmorphologic examination, use of electronic databases and genetic/molecular investigations. The aim of this workup is to reach an etiologic diagnosis which is a prerequisite for both establishing prognosis and adequate therapy and genetic counseling.