ABSTRACT: Previously, chromosomal anomalies and, to a lesser extent, other congenital anomalies have been associated with an increased risk of celiac disease (CD). We investigated these associations using a systematic approach. We identified all of the singleton children (792,401) born in Sweden between 1987 and 1993, and obtained cases of CD using the Swedish National Inpatient Registry. We applied Cox regression models as well as sibling designs to study the association between congenital anomalies and childhood CD. We observed that anomalies of face, neck, ear, heart, digestive tract, or chromosomes were associated with CD.