Esophageal atresia is a common type of congenital malformation. The etiology of esophageal atresia is unclear and its pathogenesis is controversial. Because previous reports have inconsistently noted the type and frequency of malformations associated with esophageal atresia, we conducted this study in a geographically well-defined population, evaluating the birth prevalence of esophageal atresia and associated malformations ascertained between 1979 and 2003 in 334,262 consecutive births. Of the 99 patients with esophageal atresia, 46 (46.5%) had associated malformations. These included patients with chromosomal abnormalities (8 patients, 8%); non-chromosomal recognized syndromes (4 patients), including one each CHARGE syndrome, Fanconi anemia, Fryns syndrome, and Opitz G/BBB syndrome; associations including VACTERL (10 patients), and one schisis; one oculo-auriculo-vertebral spectrum; one malformation complex, a sirenomelia, and non-syndromic multiple congenital anomalies (MCA) (21 patients, 21%). Malformations of the cardiovascular system (24%), urogenital system (21%), digestive system (21%), musculoskeletal system (14%), and central nervous system (7%) were the most common other congenital malformations occurring in patients with esophageal atresia and non-syndromic MCA. We observed a high prevalence of total malformations and specific patterns of malformations associated with esophageal atresia which emphasizes the need to evaluate all patients with esophageal atresia for possible associated malformations. The malformations associated with esophageal atresia could be classified into a recognizable malformation syndrome or pattern in 25 out of 46 patients (54%).