Esophageal atresia (EA) is a congenital developmental defect of the alimentary tract concerning the interruption of the esophagus with or without connection to the trachea. The incidence of EA is 1 in 3000–3500 of live-born infants, and occurs in both isolated and syndromic (in combination with abnormalities in other organ systems) forms. The molecular mechanisms underlying the development of EA are poorly understood. Knockout studies in mice indicate that genes likeSonic hedgehog,Gli2, andGli3play a role in the etiology of EA. These facts led us to hypothesize thatSonic hedgehog-GLIgene rearrangements are associated with EA in humans. To test this hypothesis, we screened patients with isolated and syndromic EA forGLI2and/orGLI3microrearrangements using methods to estimate the copy number (Multiplex Ligation-dependent Probe Amplification, real-time polymerase chain reaction). To our best knowledge this is the first study assessing copy number ofGLI2andGLI3genes in patients with EA.