Cases with congenital diaphragmatic hernia (CDH) often have other associated anomalies. The purpose of this investigation was to assess the prevalence and the types of associated anomalies in CDH in a defined population. The anomalies associated with CDH were collected in all live births, stillbirths and terminations of pregnancy during 29 years in 386,088 consecutive pregnancies of known outcome in the area covered by our population based registry of congenital anomalies. Of the 139 cases with CDH born during this period (total prevalence of 3.60 per 10,000), 85 (61.2%) had associated major anomalies. There were 25 (18.0%) cases with chromosomal abnormalities including 12 trisomies 18, and 24 (17.3%) nonchromosomal recognized dysmorphic conditions. There were no predominant recognized dysmorphic conditions, but Fryns syndrome. However, other recognized dysmorphic conditions were registered including fetal alcohol syndrome, de Lange syndrome, sequences (laterality sequence and ectopia cordis), and complexes (limb body wall complex). Thirty six (25.9%) of the cases had non syndromic multiple congenital anomalies (MCA). Anomalies of the cardiovascular system (n = 53, 27.5%), the urogenital system (n = 34, 17.6%), the musculoskeletal system (n = 29, 15.0%), and the central nervous system (n = 19, 9.8%) were the most common other congenital anomalies. We observed specific patterns of anomalies associated with CDH which emphasizes the need to evaluate all patients with CDH for possible associated malformations. In conclusion the overall prevalence of associated anomalies, which was close to two in three infants, emphasizes the need for a thorough investigation of cases with CDH. A routine screening for other anomalies may be considered in infants and in fetuses with CDH. One should be aware that the anomalies associated with CDH can be classified into a recognizable anomaly, syndrome or pattern in more than one out of two cases with CDH.