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Esophageal atresia\/tracheoesophageal fistula (EA\/TEF) is one of the most common gastrointestinal congenital defects with an incidence rate of 1 in 2,500 births. EA\/TEF is linked to the disruption of the compartmentalization process of the foregut tube. In EA\/TEF patients, other organ anomalies and disorders have also been reported. Over the last two decades, animal models have shown the involvement of multiple signaling pathways and transcription factors in the development of the esophagus and trachea. Use of induced pluripotent stem cells (iPSCs) to understand organogenesis has been a valuable tool for mimicking gastrointestinal and respiratory organs. 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